- Posts: 12
Regarding temperature
- Navarro
- Topic Author
- Offline
- Fresh Boarder
I want to analyze the temperature dependence of the adsorption of a Protein in a bilayer membrane. For that, I'm running simulations at 300K and 328K, but the problem is that at 300K the protein barely moves (only its lateral chains beads moves a little), while at 328K the proteins moves freely.
Is this type of comparison impossible to do with MARTINI?
This is the *mdp I'm using:
integrator = md
dt = 0.01
nsteps = 20000000
nstcomm = 10
comm-grps =
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10000
nstenergy = 1000
nstxtcout = 10000
xtc_precision = 100
xtc-grps =
energygrps = Protein POPC DFMG W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
cutoff-scheme = group
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
tcoupl = Berendsen
tc-grps = Protein POPC DFMG W_NA
tau_t = 2.0 2.0 2.0 2.0
ref_t = 300 300 300 300
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 1.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
Best,
Carlos
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- floris
- Offline
- Admin
- Posts: 15
are you sure you did not accidentally define constraints (by putting or uncommenting: define = -DPOSRES in your mdp file)?
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- Navarro
- Topic Author
- Offline
- Fresh Boarder
- Posts: 12
Thanks for your reply.
What i mean is that at 300K the protein got 'stuck' in the same place during the MD simulation that i place it when i create the system with insane.
I'm completely sure that i didn't put POSRES in the *mdp, but i did use elastic network into the protein (to maintain its 'global structure' more rigid during the simulation)
This is the *itp of my protein:
; Created by py version 2.4
; Using the following options: -f cor15a_centered_renumbered.pdb -o COR15A-100%Glycerol.top -x COR15A-100%Glycerol-CG.pdb -dssp /home/krlitros87/dssp-2.0.4-linux-i386 -p backbone -ff martini22 -elastic -ef 1000 -el 0.5 -eu 0.9 -ea 0 -ep 0
; Sequence:
; AKGDGNILDDLNEATKKASDFVTDKTKEALADGEKAKDYVVEKNSETADTLGKEAEKAAAYVEEKGKEAANKAAEFAEGKAGEAKDATK
; Secondary Structure:
; CCS13332T1111HHHHHHHHHHHHH2222SCSSCCCSSSSCCSSSCCT1111HHHHH2222T1111HHHH2222TT3333CCSSSCCC
[ moleculetype ]
; Name Exclusions
Protein_A 1
[ atoms ]
1 Qd 1 ALA BB 1 1.0000 ; C
2 P5 2 LYS BB 2 0.0000 ; C
3 C3 2 LYS SC1 3 0.0000 ; C
4 Qd 2 LYS SC2 4 1.0000 ; C
5 P5 3 GLY BB 5 0.0000 ; S
6 Nd 4 ASP BB 6 0.0000 ; 1
7 Qa 4 ASP SC1 7 -1.0000 ; 1
8 Nda 5 GLY BB 8 0.0000 ; 3
9 Nda 6 ASN BB 9 0.0000 ; 3
10 P5 6 ASN SC1 10 0.0000 ; 3
11 Nda 7 ILE BB 11 0.0000 ; 3
12 AC1 7 ILE SC1 12 0.0000 ; 3
13 Na 8 LEU BB 13 0.0000 ; 2
14 AC1 8 LEU SC1 14 0.0000 ; 2
15 Nda 9 ASP BB 15 0.0000 ; T
16 Qa 9 ASP SC1 16 -1.0000 ; T
17 Nd 10 ASP BB 17 0.0000 ; 1
18 Qa 10 ASP SC1 18 -1.0000 ; 1
19 Nd 11 LEU BB 19 0.0000 ; 1
20 AC1 11 LEU SC1 20 0.0000 ; 1
21 Nd 12 ASN BB 21 0.0000 ; 1
22 P5 12 ASN SC1 22 0.0000 ; 1
23 Nd 13 GLU BB 23 0.0000 ; 1
24 Qa 13 GLU SC1 24 -1.0000 ; 1
25 C5 14 ALA BB 25 0.0000 ; H
26 N0 15 THR BB 26 0.0000 ; H
27 P1 15 THR SC1 27 0.0000 ; H
28 N0 16 LYS BB 28 0.0000 ; H
29 C3 16 LYS SC1 29 0.0000 ; H
30 Qd 16 LYS SC2 30 1.0000 ; H
31 N0 17 LYS BB 31 0.0000 ; H
32 C3 17 LYS SC1 32 0.0000 ; H
33 Qd 17 LYS SC2 33 1.0000 ; H
34 C5 18 ALA BB 34 0.0000 ; H
35 N0 19 SER BB 35 0.0000 ; H
36 P1 19 SER SC1 36 0.0000 ; H
37 N0 20 ASP BB 37 0.0000 ; H
38 Qa 20 ASP SC1 38 -1.0000 ; H
39 N0 21 PHE BB 39 0.0000 ; H
40 SC5 21 PHE SC1 40 0.0000 ; H
41 SC5 21 PHE SC2 41 0.0000 ; H
42 SC5 21 PHE SC3 42 0.0000 ; H
43 N0 22 VAL BB 43 0.0000 ; H
44 AC2 22 VAL SC1 44 0.0000 ; H
45 N0 23 THR BB 45 0.0000 ; H
46 P1 23 THR SC1 46 0.0000 ; H
47 N0 24 ASP BB 47 0.0000 ; H
48 Qa 24 ASP SC1 48 -1.0000 ; H
49 N0 25 LYS BB 49 0.0000 ; H
50 C3 25 LYS SC1 50 0.0000 ; H
51 Qd 25 LYS SC2 51 1.0000 ; H
52 N0 26 THR BB 52 0.0000 ; H
53 P1 26 THR SC1 53 0.0000 ; H
54 Na 27 LYS BB 54 0.0000 ; 2
55 C3 27 LYS SC1 55 0.0000 ; 2
56 Qd 27 LYS SC2 56 1.0000 ; 2
57 Na 28 GLU BB 57 0.0000 ; 2
58 Qa 28 GLU SC1 58 -1.0000 ; 2
59 N0 29 ALA BB 59 0.0000 ; 2
60 Na 30 LEU BB 60 0.0000 ; 2
61 AC1 30 LEU SC1 61 0.0000 ; 2
62 P4 31 ALA BB 62 0.0000 ; S
63 P5 32 ASP BB 63 0.0000 ; C
64 Qa 32 ASP SC1 64 -1.0000 ; C
65 P5 33 GLY BB 65 0.0000 ; S
66 P5 34 GLU BB 66 0.0000 ; S
67 Qa 34 GLU SC1 67 -1.0000 ; S
68 P5 35 LYS BB 68 0.0000 ; C
69 C3 35 LYS SC1 69 0.0000 ; C
70 Qd 35 LYS SC2 70 1.0000 ; C
71 P4 36 ALA BB 71 0.0000 ; C
72 P5 37 LYS BB 72 0.0000 ; C
73 C3 37 LYS SC1 73 0.0000 ; C
74 Qd 37 LYS SC2 74 1.0000 ; C
75 P5 38 ASP BB 75 0.0000 ; S
76 Qa 38 ASP SC1 76 -1.0000 ; S
77 P5 39 TYR BB 77 0.0000 ; S
78 SC4 39 TYR SC1 78 0.0000 ; S
79 SC4 39 TYR SC2 79 0.0000 ; S
80 SP1 39 TYR SC3 80 0.0000 ; S
81 P5 40 VAL BB 81 0.0000 ; S
82 AC2 40 VAL SC1 82 0.0000 ; S
83 P5 41 VAL BB 83 0.0000 ; S
84 AC2 41 VAL SC1 84 0.0000 ; S
85 P5 42 GLU BB 85 0.0000 ; C
86 Qa 42 GLU SC1 86 -1.0000 ; C
87 P5 43 LYS BB 87 0.0000 ; C
88 C3 43 LYS SC1 88 0.0000 ; C
89 Qd 43 LYS SC2 89 1.0000 ; C
90 P5 44 ASN BB 90 0.0000 ; S
91 P5 44 ASN SC1 91 0.0000 ; S
92 P5 45 SER BB 92 0.0000 ; S
93 P1 45 SER SC1 93 0.0000 ; S
94 P5 46 GLU BB 94 0.0000 ; S
95 Qa 46 GLU SC1 95 -1.0000 ; S
96 P5 47 THR BB 96 0.0000 ; C
97 P1 47 THR SC1 97 0.0000 ; C
98 P4 48 ALA BB 98 0.0000 ; C
99 Nda 49 ASP BB 99 0.0000 ; T
100 Qa 49 ASP SC1 100 -1.0000 ; T
101 Nd 50 THR BB 101 0.0000 ; 1
102 P1 50 THR SC1 102 0.0000 ; 1
103 Nd 51 LEU BB 103 0.0000 ; 1
104 AC1 51 LEU SC1 104 0.0000 ; 1
105 Nd 52 GLY BB 105 0.0000 ; 1
106 Nd 53 LYS BB 106 0.0000 ; 1
107 C3 53 LYS SC1 107 0.0000 ; 1
108 Qd 53 LYS SC2 108 1.0000 ; 1
109 N0 54 GLU BB 109 0.0000 ; H
110 Qa 54 GLU SC1 110 -1.0000 ; H
111 C5 55 ALA BB 111 0.0000 ; H
112 N0 56 GLU BB 112 0.0000 ; H
113 Qa 56 GLU SC1 113 -1.0000 ; H
114 N0 57 LYS BB 114 0.0000 ; H
115 C3 57 LYS SC1 115 0.0000 ; H
116 Qd 57 LYS SC2 116 1.0000 ; H
117 C5 58 ALA BB 117 0.0000 ; H
118 N0 59 ALA BB 118 0.0000 ; 2
119 N0 60 ALA BB 119 0.0000 ; 2
120 Na 61 TYR BB 120 0.0000 ; 2
121 SC4 61 TYR SC1 121 0.0000 ; 2
122 SC4 61 TYR SC2 122 0.0000 ; 2
123 SP1 61 TYR SC3 123 0.0000 ; 2
124 Na 62 VAL BB 124 0.0000 ; 2
125 AC2 62 VAL SC1 125 0.0000 ; 2
126 Nda 63 GLU BB 126 0.0000 ; T
127 Qa 63 GLU SC1 127 -1.0000 ; T
128 Nd 64 GLU BB 128 0.0000 ; 1
129 Qa 64 GLU SC1 129 -1.0000 ; 1
130 Nd 65 LYS BB 130 0.0000 ; 1
131 C3 65 LYS SC1 131 0.0000 ; 1
132 Qd 65 LYS SC2 132 1.0000 ; 1
133 Nd 66 GLY BB 133 0.0000 ; 1
134 Nd 67 LYS BB 134 0.0000 ; 1
135 C3 67 LYS SC1 135 0.0000 ; 1
136 Qd 67 LYS SC2 136 1.0000 ; 1
137 N0 68 GLU BB 137 0.0000 ; H
138 Qa 68 GLU SC1 138 -1.0000 ; H
139 C5 69 ALA BB 139 0.0000 ; H
140 C5 70 ALA BB 140 0.0000 ; H
141 N0 71 ASN BB 141 0.0000 ; H
142 P5 71 ASN SC1 142 0.0000 ; H
143 Na 72 LYS BB 143 0.0000 ; 2
144 C3 72 LYS SC1 144 0.0000 ; 2
145 Qd 72 LYS SC2 145 1.0000 ; 2
146 N0 73 ALA BB 146 0.0000 ; 2
147 N0 74 ALA BB 147 0.0000 ; 2
148 Na 75 GLU BB 148 0.0000 ; 2
149 Qa 75 GLU SC1 149 -1.0000 ; 2
150 Nda 76 PHE BB 150 0.0000 ; T
151 SC5 76 PHE SC1 151 0.0000 ; T
152 SC5 76 PHE SC2 152 0.0000 ; T
153 SC5 76 PHE SC3 153 0.0000 ; T
154 N0 77 ALA BB 154 0.0000 ; T
155 Nda 78 GLU BB 155 0.0000 ; 3
156 Qa 78 GLU SC1 156 -1.0000 ; 3
157 Nda 79 GLY BB 157 0.0000 ; 3
158 Nda 80 LYS BB 158 0.0000 ; 3
159 C3 80 LYS SC1 159 0.0000 ; 3
160 Qd 80 LYS SC2 160 1.0000 ; 3
161 N0 81 ALA BB 161 0.0000 ; 3
162 P5 82 GLY BB 162 0.0000 ; C
163 P5 83 GLU BB 163 0.0000 ; C
164 Qa 83 GLU SC1 164 -1.0000 ; C
165 P4 84 ALA BB 165 0.0000 ; S
166 P5 85 LYS BB 166 0.0000 ; S
167 C3 85 LYS SC1 167 0.0000 ; S
168 Qd 85 LYS SC2 168 1.0000 ; S
169 P5 86 ASP BB 169 0.0000 ; S
170 Qa 86 ASP SC1 170 -1.0000 ; S
171 P4 87 ALA BB 171 0.0000 ; C
172 P5 88 THR BB 172 0.0000 ; C
173 P1 88 THR SC1 173 0.0000 ; C
174 Qa 89 LYS BB 174 -1.0000 ; C
175 C3 89 LYS SC1 175 0.0000 ; C
176 Qd 89 LYS SC2 176 1.0000 ; C
[ bonds ]
; Backbone bonds
1 2 1 0.35000 1250 ; ALA(C)-LYS(C)
2 5 1 0.35000 1250 ; LYS(C)-GLY(S)
62 63 1 0.35000 1250 ; ALA(S)-ASP(C)
63 65 1 0.35000 1250 ; ASP(C)-GLY(S)
65 66 1 0.35000 1250 ; GLY(S)-GLU(S)
66 68 1 0.35000 1250 ; GLU(S)-LYS(C)
68 71 1 0.35000 1250 ; LYS(C)-ALA(C)
71 72 1 0.35000 1250 ; ALA(C)-LYS(C)
72 75 1 0.35000 1250 ; LYS(C)-ASP(S)
75 77 1 0.35000 1250 ; ASP(S)-TYR(S)
77 81 1 0.35000 1250 ; TYR(S)-VAL(S)
81 83 1 0.35000 1250 ; VAL(S)-VAL(S)
83 85 1 0.35000 1250 ; VAL(S)-GLU(C)
85 87 1 0.35000 1250 ; GLU(C)-LYS(C)
87 90 1 0.35000 1250 ; LYS(C)-ASN(S)
90 92 1 0.35000 1250 ; ASN(S)-SER(S)
92 94 1 0.35000 1250 ; SER(S)-GLU(S)
94 96 1 0.35000 1250 ; GLU(S)-THR(C)
96 98 1 0.35000 1250 ; THR(C)-ALA(C)
98 99 1 0.35000 1250 ; ALA(C)-ASP(T)
150 154 1 0.35000 1250 ; PHE(T)-ALA(T)
162 163 1 0.35000 1250 ; GLY(C)-GLU(C)
163 165 1 0.35000 1250 ; GLU(C)-ALA(S)
165 166 1 0.35000 1250 ; ALA(S)-LYS(S)
166 169 1 0.35000 1250 ; LYS(S)-ASP(S)
169 171 1 0.35000 1250 ; ASP(S)-ALA(C)
171 172 1 0.35000 1250 ; ALA(C)-THR(C)
172 174 1 0.35000 1250 ; THR(C)-LYS(C)
#ifndef NO_RUBBER_BANDS
#ifndef RUBBER_FC
#define RUBBER_FC 1000.000000
#endif
1 6 6 0.60951 RUBBER_FC*1.000000
1 8 6 0.68405 RUBBER_FC*1.000000
1 9 6 0.73337 RUBBER_FC*1.000000
1 133 6 0.82494 RUBBER_FC*1.000000
1 137 6 0.75963 RUBBER_FC*1.000000
1 139 6 0.45702 RUBBER_FC*1.000000
1 140 6 0.66808 RUBBER_FC*1.000000
1 141 6 0.77575 RUBBER_FC*1.000000
1 143 6 0.57739 RUBBER_FC*1.000000
1 146 6 0.55213 RUBBER_FC*1.000000
1 150 6 0.79096 RUBBER_FC*1.000000
2 8 6 0.75996 RUBBER_FC*1.000000
2 9 6 0.80125 RUBBER_FC*1.000000
2 139 6 0.80541 RUBBER_FC*1.000000
2 143 6 0.81558 RUBBER_FC*1.000000
2 146 6 0.68746 RUBBER_FC*1.000000
2 150 6 0.78818 RUBBER_FC*1.000000
5 9 6 0.50201 RUBBER_FC*1.000000
5 11 6 0.61800 RUBBER_FC*1.000000
5 13 6 0.85961 RUBBER_FC*1.000000
5 139 6 0.87458 RUBBER_FC*1.000000
6 11 6 0.54485 RUBBER_FC*1.000000
6 13 6 0.70555 RUBBER_FC*1.000000
6 15 6 0.85286 RUBBER_FC*1.000000
8 13 6 0.49605 RUBBER_FC*1.000000
8 15 6 0.57421 RUBBER_FC*1.000000
8 17 6 0.75705 RUBBER_FC*1.000000
8 19 6 0.89534 RUBBER_FC*1.000000
9 15 6 0.44014 RUBBER_FC*1.000000
9 17 6 0.49058 RUBBER_FC*1.000000
9 19 6 0.61102 RUBBER_FC*1.000000
9 21 6 0.81464 RUBBER_FC*1.000000
11 17 6 0.58976 RUBBER_FC*1.000000
11 19 6 0.55113 RUBBER_FC*1.000000
11 21 6 0.72063 RUBBER_FC*1.000000
13 19 6 0.59913 RUBBER_FC*1.000000
13 21 6 0.62549 RUBBER_FC*1.000000
13 23 6 0.80874 RUBBER_FC*1.000000
15 21 6 0.50436 RUBBER_FC*1.000000
15 23 6 0.57953 RUBBER_FC*1.000000
15 25 6 0.79192 RUBBER_FC*1.000000
17 23 6 0.46148 RUBBER_FC*1.000000
17 25 6 0.53916 RUBBER_FC*1.000000
17 26 6 0.77429 RUBBER_FC*1.000000
19 25 6 0.50260 RUBBER_FC*1.000000
19 26 6 0.61162 RUBBER_FC*1.000000
19 28 6 0.82113 RUBBER_FC*1.000000
21 26 6 0.48196 RUBBER_FC*1.000000
21 28 6 0.59665 RUBBER_FC*1.000000
21 31 6 0.82345 RUBBER_FC*1.000000
23 28 6 0.48210 RUBBER_FC*1.000000
23 31 6 0.60666 RUBBER_FC*1.000000
23 34 6 0.79433 RUBBER_FC*1.000000
25 31 6 0.51983 RUBBER_FC*1.000000
25 34 6 0.58813 RUBBER_FC*1.000000
25 35 6 0.83045 RUBBER_FC*1.000000
25 114 6 0.87135 RUBBER_FC*1.000000
26 34 6 0.47792 RUBBER_FC*1.000000
26 35 6 0.61055 RUBBER_FC*1.000000
26 37 6 0.82897 RUBBER_FC*1.000000
28 35 6 0.48360 RUBBER_FC*1.000000
28 37 6 0.62140 RUBBER_FC*1.000000
28 39 6 0.83071 RUBBER_FC*1.000000
31 37 6 0.47216 RUBBER_FC*1.000000
31 39 6 0.60104 RUBBER_FC*1.000000
31 43 6 0.82313 RUBBER_FC*1.000000
31 114 6 0.87520 RUBBER_FC*1.000000
34 39 6 0.51728 RUBBER_FC*1.000000
34 43 6 0.64763 RUBBER_FC*1.000000
34 45 6 0.85524 RUBBER_FC*1.000000
35 43 6 0.50397 RUBBER_FC*1.000000
35 45 6 0.61334 RUBBER_FC*1.000000
35 47 6 0.81463 RUBBER_FC*1.000000
37 45 6 0.48646 RUBBER_FC*1.000000
37 47 6 0.58441 RUBBER_FC*1.000000
37 49 6 0.79079 RUBBER_FC*1.000000
39 47 6 0.48490 RUBBER_FC*1.000000
39 49 6 0.57923 RUBBER_FC*1.000000
39 52 6 0.79380 RUBBER_FC*1.000000
43 49 6 0.50085 RUBBER_FC*1.000000
43 52 6 0.61170 RUBBER_FC*1.000000
43 54 6 0.83653 RUBBER_FC*1.000000
45 52 6 0.48732 RUBBER_FC*1.000000
45 54 6 0.63325 RUBBER_FC*1.000000
45 57 6 0.84925 RUBBER_FC*1.000000
47 54 6 0.47554 RUBBER_FC*1.000000
47 57 6 0.60210 RUBBER_FC*1.000000
47 59 6 0.78929 RUBBER_FC*1.000000
49 57 6 0.47813 RUBBER_FC*1.000000
49 59 6 0.57666 RUBBER_FC*1.000000
49 60 6 0.83550 RUBBER_FC*1.000000
49 62 6 0.89669 RUBBER_FC*1.000000
49 81 6 0.77474 RUBBER_FC*1.000000
49 83 6 0.67015 RUBBER_FC*1.000000
52 59 6 0.47341 RUBBER_FC*1.000000
52 60 6 0.63988 RUBBER_FC*1.000000
52 62 6 0.76749 RUBBER_FC*1.000000
52 83 6 0.86836 RUBBER_FC*1.000000
54 60 6 0.49864 RUBBER_FC*1.000000
54 62 6 0.50379 RUBBER_FC*1.000000
54 63 6 0.86342 RUBBER_FC*1.000000
57 62 6 0.47141 RUBBER_FC*1.000000
57 63 6 0.71717 RUBBER_FC*1.000000
57 68 6 0.89292 RUBBER_FC*1.000000
57 71 6 0.75493 RUBBER_FC*1.000000
57 77 6 0.86366 RUBBER_FC*1.000000
57 81 6 0.65010 RUBBER_FC*1.000000
57 83 6 0.62097 RUBBER_FC*1.000000
59 63 6 0.76568 RUBBER_FC*1.000000
59 68 6 0.83933 RUBBER_FC*1.000000
59 71 6 0.79847 RUBBER_FC*1.000000
59 81 6 0.83027 RUBBER_FC*1.000000
59 83 6 0.67445 RUBBER_FC*1.000000
60 65 6 0.86984 RUBBER_FC*1.000000
62 66 6 0.87636 RUBBER_FC*1.000000
63 68 6 0.69245 RUBBER_FC*1.000000
63 71 6 0.77627 RUBBER_FC*1.000000
65 71 6 0.75392 RUBBER_FC*1.000000
68 81 6 0.89544 RUBBER_FC*1.000000
68 83 6 0.85968 RUBBER_FC*1.000000
71 77 6 0.70169 RUBBER_FC*1.000000
71 81 6 0.57629 RUBBER_FC*1.000000
71 83 6 0.60588 RUBBER_FC*1.000000
71 85 6 0.77852 RUBBER_FC*1.000000
72 81 6 0.45853 RUBBER_FC*1.000000
72 83 6 0.45173 RUBBER_FC*1.000000
72 85 6 0.48102 RUBBER_FC*1.000000
72 87 6 0.54622 RUBBER_FC*1.000000
72 90 6 0.88254 RUBBER_FC*1.000000
72 94 6 0.87816 RUBBER_FC*1.000000
72 96 6 0.78234 RUBBER_FC*1.000000
72 98 6 0.66732 RUBBER_FC*1.000000
72 99 6 0.82117 RUBBER_FC*1.000000
72 101 6 0.85384 RUBBER_FC*1.000000
75 83 6 0.54981 RUBBER_FC*1.000000
75 85 6 0.63177 RUBBER_FC*1.000000
75 87 6 0.70190 RUBBER_FC*1.000000
75 94 6 0.86122 RUBBER_FC*1.000000
75 96 6 0.64844 RUBBER_FC*1.000000
75 98 6 0.47786 RUBBER_FC*1.000000
75 99 6 0.51856 RUBBER_FC*1.000000
75 101 6 0.60791 RUBBER_FC*1.000000
75 103 6 0.86290 RUBBER_FC*1.000000
77 85 6 0.82562 RUBBER_FC*1.000000
77 98 6 0.69172 RUBBER_FC*1.000000
77 99 6 0.53199 RUBBER_FC*1.000000
77 101 6 0.55060 RUBBER_FC*1.000000
77 103 6 0.86260 RUBBER_FC*1.000000
77 106 6 0.85642 RUBBER_FC*1.000000
81 87 6 0.81756 RUBBER_FC*1.000000
81 98 6 0.72681 RUBBER_FC*1.000000
81 99 6 0.68272 RUBBER_FC*1.000000
81 101 6 0.59599 RUBBER_FC*1.000000
81 103 6 0.89447 RUBBER_FC*1.000000
83 98 6 0.79917 RUBBER_FC*1.000000
83 99 6 0.87398 RUBBER_FC*1.000000
83 101 6 0.73730 RUBBER_FC*1.000000
85 92 6 0.87215 RUBBER_FC*1.000000
85 98 6 0.69711 RUBBER_FC*1.000000
85 101 6 0.80460 RUBBER_FC*1.000000
87 94 6 0.66812 RUBBER_FC*1.000000
87 96 6 0.75375 RUBBER_FC*1.000000
87 98 6 0.63762 RUBBER_FC*1.000000
90 96 6 0.83435 RUBBER_FC*1.000000
90 98 6 0.84658 RUBBER_FC*1.000000
92 98 6 0.75169 RUBBER_FC*1.000000
96 101 6 0.86074 RUBBER_FC*1.000000
98 103 6 0.57668 RUBBER_FC*1.000000
98 105 6 0.74909 RUBBER_FC*1.000000
99 105 6 0.49394 RUBBER_FC*1.000000
99 106 6 0.63804 RUBBER_FC*1.000000
99 109 6 0.83973 RUBBER_FC*1.000000
101 106 6 0.47150 RUBBER_FC*1.000000
101 109 6 0.62297 RUBBER_FC*1.000000
101 111 6 0.80748 RUBBER_FC*1.000000
103 109 6 0.49761 RUBBER_FC*1.000000
103 111 6 0.57294 RUBBER_FC*1.000000
103 112 6 0.86267 RUBBER_FC*1.000000
105 111 6 0.45563 RUBBER_FC*1.000000
105 112 6 0.65617 RUBBER_FC*1.000000
105 114 6 0.86880 RUBBER_FC*1.000000
106 112 6 0.61836 RUBBER_FC*1.000000
106 114 6 0.75291 RUBBER_FC*1.000000
109 114 6 0.52963 RUBBER_FC*1.000000
109 117 6 0.67274 RUBBER_FC*1.000000
109 118 6 0.87058 RUBBER_FC*1.000000
111 117 6 0.49775 RUBBER_FC*1.000000
111 118 6 0.59568 RUBBER_FC*1.000000
111 119 6 0.87972 RUBBER_FC*1.000000
112 118 6 0.49306 RUBBER_FC*1.000000
112 119 6 0.64482 RUBBER_FC*1.000000
112 120 6 0.84062 RUBBER_FC*1.000000
114 119 6 0.64352 RUBBER_FC*1.000000
114 120 6 0.70494 RUBBER_FC*1.000000
117 120 6 0.53903 RUBBER_FC*1.000000
117 124 6 0.63744 RUBBER_FC*1.000000
117 126 6 0.82639 RUBBER_FC*1.000000
118 124 6 0.54079 RUBBER_FC*1.000000
118 126 6 0.60574 RUBBER_FC*1.000000
118 128 6 0.78911 RUBBER_FC*1.000000
118 130 6 0.89099 RUBBER_FC*1.000000
119 126 6 0.50969 RUBBER_FC*1.000000
119 128 6 0.53704 RUBBER_FC*1.000000
119 130 6 0.62095 RUBBER_FC*1.000000
119 133 6 0.81928 RUBBER_FC*1.000000
120 128 6 0.55376 RUBBER_FC*1.000000
120 130 6 0.46921 RUBBER_FC*1.000000
120 133 6 0.60744 RUBBER_FC*1.000000
120 134 6 0.85526 RUBBER_FC*1.000000
124 130 6 0.55800 RUBBER_FC*1.000000
124 133 6 0.51991 RUBBER_FC*1.000000
124 134 6 0.76937 RUBBER_FC*1.000000
126 133 6 0.45902 RUBBER_FC*1.000000
126 134 6 0.59486 RUBBER_FC*1.000000
126 137 6 0.81220 RUBBER_FC*1.000000
126 139 6 0.89450 RUBBER_FC*1.000000
128 134 6 0.47872 RUBBER_FC*1.000000
128 137 6 0.61104 RUBBER_FC*1.000000
128 139 6 0.79438 RUBBER_FC*1.000000
130 137 6 0.47971 RUBBER_FC*1.000000
130 139 6 0.56675 RUBBER_FC*1.000000
130 140 6 0.80006 RUBBER_FC*1.000000
133 139 6 0.44262 RUBBER_FC*1.000000
133 140 6 0.58090 RUBBER_FC*1.000000
133 141 6 0.81630 RUBBER_FC*1.000000
134 140 6 0.45504 RUBBER_FC*1.000000
134 141 6 0.61660 RUBBER_FC*1.000000
134 143 6 0.81587 RUBBER_FC*1.000000
137 141 6 0.47991 RUBBER_FC*1.000000
137 143 6 0.59263 RUBBER_FC*1.000000
137 146 6 0.78985 RUBBER_FC*1.000000
139 143 6 0.51064 RUBBER_FC*1.000000
139 146 6 0.60477 RUBBER_FC*1.000000
139 147 6 0.87337 RUBBER_FC*1.000000
140 146 6 0.49461 RUBBER_FC*1.000000
140 147 6 0.66965 RUBBER_FC*1.000000
140 148 6 0.87928 RUBBER_FC*1.000000
141 147 6 0.48963 RUBBER_FC*1.000000
141 148 6 0.63138 RUBBER_FC*1.000000
141 150 6 0.80630 RUBBER_FC*1.000000
143 148 6 0.46729 RUBBER_FC*1.000000
143 150 6 0.54569 RUBBER_FC*1.000000
143 154 6 0.85981 RUBBER_FC*1.000000
143 157 6 0.89133 RUBBER_FC*1.000000
146 150 6 0.49440 RUBBER_FC*1.000000
146 154 6 0.75432 RUBBER_FC*1.000000
146 155 6 0.83232 RUBBER_FC*1.000000
146 157 6 0.89001 RUBBER_FC*1.000000
147 154 6 0.64392 RUBBER_FC*1.000000
147 155 6 0.57728 RUBBER_FC*1.000000
147 157 6 0.58549 RUBBER_FC*1.000000
147 158 6 0.82144 RUBBER_FC*1.000000
148 155 6 0.51872 RUBBER_FC*1.000000
148 157 6 0.44313 RUBBER_FC*1.000000
148 158 6 0.57754 RUBBER_FC*1.000000
148 161 6 0.82709 RUBBER_FC*1.000000
150 157 6 0.66668 RUBBER_FC*1.000000
150 158 6 0.70200 RUBBER_FC*1.000000
150 161 6 0.88565 RUBBER_FC*1.000000
154 158 6 0.52010 RUBBER_FC*1.000000
154 161 6 0.58433 RUBBER_FC*1.000000
154 162 6 0.82688 RUBBER_FC*1.000000
155 161 6 0.45952 RUBBER_FC*1.000000
155 162 6 0.58692 RUBBER_FC*1.000000
157 162 6 0.50005 RUBBER_FC*1.000000
157 163 6 0.78828 RUBBER_FC*1.000000
157 169 6 0.88570 RUBBER_FC*1.000000
158 163 6 0.75174 RUBBER_FC*1.000000
158 169 6 0.75248 RUBBER_FC*1.000000
158 171 6 0.86992 RUBBER_FC*1.000000
158 174 6 0.75673 RUBBER_FC*1.000000
161 169 6 0.74990 RUBBER_FC*1.000000
161 171 6 0.76791 RUBBER_FC*1.000000
161 172 6 0.79313 RUBBER_FC*1.000000
161 174 6 0.66911 RUBBER_FC*1.000000
162 166 6 0.70613 RUBBER_FC*1.000000
162 169 6 0.55856 RUBBER_FC*1.000000
162 171 6 0.66607 RUBBER_FC*1.000000
162 172 6 0.82301 RUBBER_FC*1.000000
162 174 6 0.83544 RUBBER_FC*1.000000
163 169 6 0.43636 RUBBER_FC*1.000000
163 171 6 0.54826 RUBBER_FC*1.000000
163 172 6 0.79784 RUBBER_FC*1.000000
165 171 6 0.59236 RUBBER_FC*1.000000
169 174 6 0.80398 RUBBER_FC*1.000000
#endif
; Sidechain bonds
2 3 1 0.33000 5000 ; LYS
3 4 1 0.28000 5000 ; LYS
6 7 1 0.32000 7500 ; ASP
9 10 1 0.32000 5000 ; ASN
13 14 1 0.33000 7500 ; LEU
15 16 1 0.32000 7500 ; ASP
17 18 1 0.32000 7500 ; ASP
19 20 1 0.33000 7500 ; LEU
21 22 1 0.32000 5000 ; ASN
23 24 1 0.40000 5000 ; GLU
28 29 1 0.33000 5000 ; LYS
29 30 1 0.28000 5000 ; LYS
31 32 1 0.33000 5000 ; LYS
32 33 1 0.28000 5000 ; LYS
35 36 1 0.25000 7500 ; SER
37 38 1 0.32000 7500 ; ASP
39 40 1 0.31000 7500 ; PHE
47 48 1 0.32000 7500 ; ASP
49 50 1 0.33000 5000 ; LYS
50 51 1 0.28000 5000 ; LYS
54 55 1 0.33000 5000 ; LYS
55 56 1 0.28000 5000 ; LYS
57 58 1 0.40000 5000 ; GLU
60 61 1 0.33000 7500 ; LEU
63 64 1 0.32000 7500 ; ASP
66 67 1 0.40000 5000 ; GLU
68 69 1 0.33000 5000 ; LYS
69 70 1 0.28000 5000 ; LYS
72 73 1 0.33000 5000 ; LYS
73 74 1 0.28000 5000 ; LYS
75 76 1 0.32000 7500 ; ASP
77 78 1 0.32000 5000 ; TYR
85 86 1 0.40000 5000 ; GLU
87 88 1 0.33000 5000 ; LYS
88 89 1 0.28000 5000 ; LYS
90 91 1 0.32000 5000 ; ASN
92 93 1 0.25000 7500 ; SER
94 95 1 0.40000 5000 ; GLU
99 100 1 0.32000 7500 ; ASP
103 104 1 0.33000 7500 ; LEU
106 107 1 0.33000 5000 ; LYS
107 108 1 0.28000 5000 ; LYS
109 110 1 0.40000 5000 ; GLU
112 113 1 0.40000 5000 ; GLU
114 115 1 0.33000 5000 ; LYS
115 116 1 0.28000 5000 ; LYS
120 121 1 0.32000 5000 ; TYR
126 127 1 0.40000 5000 ; GLU
128 129 1 0.40000 5000 ; GLU
130 131 1 0.33000 5000 ; LYS
131 132 1 0.28000 5000 ; LYS
134 135 1 0.33000 5000 ; LYS
135 136 1 0.28000 5000 ; LYS
137 138 1 0.40000 5000 ; GLU
141 142 1 0.32000 5000 ; ASN
143 144 1 0.33000 5000 ; LYS
144 145 1 0.28000 5000 ; LYS
148 149 1 0.40000 5000 ; GLU
150 151 1 0.31000 7500 ; PHE
155 156 1 0.40000 5000 ; GLU
158 159 1 0.33000 5000 ; LYS
159 160 1 0.28000 5000 ; LYS
163 164 1 0.40000 5000 ; GLU
166 167 1 0.33000 5000 ; LYS
167 168 1 0.28000 5000 ; LYS
169 170 1 0.32000 7500 ; ASP
174 175 1 0.33000 5000 ; LYS
175 176 1 0.28000 5000 ; LYS
[ constraints ]
5 6 1 0.33000 ; GLY(S)-ASP(1)
6 8 1 0.31000 ; ASP(1)-GLY(3)
8 9 1 0.31000 ; GLY(3)-ASN(3)
9 11 1 0.31000 ; ASN(3)-ILE(3)
11 13 1 0.31000 ; ILE(3)-LEU(2)
13 15 1 0.33000 ; LEU(2)-ASP(T)
15 17 1 0.33000 ; ASP(T)-ASP(1)
17 19 1 0.31000 ; ASP(1)-LEU(1)
19 21 1 0.31000 ; LEU(1)-ASN(1)
21 23 1 0.31000 ; ASN(1)-GLU(1)
23 25 1 0.31000 ; GLU(1)-ALA(H)
25 26 1 0.31000 ; ALA(H)-THR(H)
26 28 1 0.31000 ; THR(H)-LYS(H)
28 31 1 0.31000 ; LYS(H)-LYS(H)
31 34 1 0.31000 ; LYS(H)-ALA(H)
34 35 1 0.31000 ; ALA(H)-SER(H)
35 37 1 0.31000 ; SER(H)-ASP(H)
37 39 1 0.31000 ; ASP(H)-PHE(H)
39 43 1 0.31000 ; PHE(H)-VAL(H)
43 45 1 0.31000 ; VAL(H)-THR(H)
45 47 1 0.31000 ; THR(H)-ASP(H)
47 49 1 0.31000 ; ASP(H)-LYS(H)
49 52 1 0.31000 ; LYS(H)-THR(H)
52 54 1 0.31000 ; THR(H)-LYS(2)
54 57 1 0.31000 ; LYS(2)-GLU(2)
57 59 1 0.31000 ; GLU(2)-ALA(2)
59 60 1 0.31000 ; ALA(2)-LEU(2)
60 62 1 0.33000 ; LEU(2)-ALA(S)
99 101 1 0.33000 ; ASP(T)-THR(1)
101 103 1 0.31000 ; THR(1)-LEU(1)
103 105 1 0.31000 ; LEU(1)-GLY(1)
105 106 1 0.31000 ; GLY(1)-LYS(1)
106 109 1 0.31000 ; LYS(1)-GLU(H)
109 111 1 0.31000 ; GLU(H)-ALA(H)
111 112 1 0.31000 ; ALA(H)-GLU(H)
112 114 1 0.31000 ; GLU(H)-LYS(H)
114 117 1 0.31000 ; LYS(H)-ALA(H)
117 118 1 0.31000 ; ALA(H)-ALA(2)
118 119 1 0.31000 ; ALA(2)-ALA(2)
119 120 1 0.31000 ; ALA(2)-TYR(2)
120 124 1 0.31000 ; TYR(2)-VAL(2)
124 126 1 0.33000 ; VAL(2)-GLU(T)
126 128 1 0.33000 ; GLU(T)-GLU(1)
128 130 1 0.31000 ; GLU(1)-LYS(1)
130 133 1 0.31000 ; LYS(1)-GLY(1)
133 134 1 0.31000 ; GLY(1)-LYS(1)
134 137 1 0.31000 ; LYS(1)-GLU(H)
137 139 1 0.31000 ; GLU(H)-ALA(H)
139 140 1 0.31000 ; ALA(H)-ALA(H)
140 141 1 0.31000 ; ALA(H)-ASN(H)
141 143 1 0.31000 ; ASN(H)-LYS(2)
143 146 1 0.31000 ; LYS(2)-ALA(2)
146 147 1 0.31000 ; ALA(2)-ALA(2)
147 148 1 0.31000 ; ALA(2)-GLU(2)
148 150 1 0.33000 ; GLU(2)-PHE(T)
154 155 1 0.33000 ; ALA(T)-GLU(3)
155 157 1 0.31000 ; GLU(3)-GLY(3)
157 158 1 0.31000 ; GLY(3)-LYS(3)
158 161 1 0.31000 ; LYS(3)-ALA(3)
161 162 1 0.33000 ; ALA(3)-GLY(C)
11 12 1 0.31000 ; ILE
26 27 1 0.26000 ; THR
40 41 1 0.27000 ; PHE
40 42 1 0.27000 ; PHE
41 42 1 0.27000 ; PHE
43 44 1 0.26500 ; VAL
45 46 1 0.26000 ; THR
52 53 1 0.26000 ; THR
78 79 1 0.27000 ; TYR
78 80 1 0.27000 ; TYR
79 80 1 0.27000 ; TYR
81 82 1 0.26500 ; VAL
83 84 1 0.26500 ; VAL
96 97 1 0.26000 ; THR
101 102 1 0.26000 ; THR
121 122 1 0.27000 ; TYR
121 123 1 0.27000 ; TYR
122 123 1 0.27000 ; TYR
124 125 1 0.26500 ; VAL
151 152 1 0.27000 ; PHE
151 153 1 0.27000 ; PHE
152 153 1 0.27000 ; PHE
172 173 1 0.26000 ; THR
[ angles ]
; Backbone angles
1 2 5 2 127 20 ; ALA(C)-LYS(C)-GLY(S)
2 5 6 2 127 20 ; LYS(C)-GLY(S)-ASP(1)
5 6 8 2 130 20 ; GLY(S)-ASP(1)-GLY(3)
6 8 9 2 96 700 ; ASP(1)-GLY(3)-ASN(3)
8 9 11 2 96 700 ; GLY(3)-ASN(3)-ILE(3)
9 11 13 2 96 700 ; ASN(3)-ILE(3)-LEU(2)
11 13 15 2 100 20 ; ILE(3)-LEU(2)-ASP(T)
13 15 17 2 100 20 ; LEU(2)-ASP(T)-ASP(1)
15 17 19 2 100 20 ; ASP(T)-ASP(1)-LEU(1)
17 19 21 2 96 700 ; ASP(1)-LEU(1)-ASN(1)
19 21 23 2 96 700 ; LEU(1)-ASN(1)-GLU(1)
21 23 25 2 96 700 ; ASN(1)-GLU(1)-ALA(H)
23 25 26 2 96 700 ; GLU(1)-ALA(H)-THR(H)
25 26 28 2 96 700 ; ALA(H)-THR(H)-LYS(H)
26 28 31 2 96 700 ; THR(H)-LYS(H)-LYS(H)
28 31 34 2 96 700 ; LYS(H)-LYS(H)-ALA(H)
31 34 35 2 96 700 ; LYS(H)-ALA(H)-SER(H)
34 35 37 2 96 700 ; ALA(H)-SER(H)-ASP(H)
35 37 39 2 96 700 ; SER(H)-ASP(H)-PHE(H)
37 39 43 2 96 700 ; ASP(H)-PHE(H)-VAL(H)
39 43 45 2 96 700 ; PHE(H)-VAL(H)-THR(H)
43 45 47 2 96 700 ; VAL(H)-THR(H)-ASP(H)
45 47 49 2 96 700 ; THR(H)-ASP(H)-LYS(H)
47 49 52 2 96 700 ; ASP(H)-LYS(H)-THR(H)
49 52 54 2 96 700 ; LYS(H)-THR(H)-LYS(2)
52 54 57 2 96 700 ; THR(H)-LYS(2)-GLU(2)
54 57 59 2 96 700 ; LYS(2)-GLU(2)-ALA(2)
57 59 60 2 96 700 ; GLU(2)-ALA(2)-LEU(2)
59 60 62 2 130 20 ; ALA(2)-LEU(2)-ALA(S)
60 62 63 2 127 20 ; LEU(2)-ALA(S)-ASP(C)
62 63 65 2 127 20 ; ALA(S)-ASP(C)-GLY(S)
63 65 66 2 127 20 ; ASP(C)-GLY(S)-GLU(S)
65 66 68 2 127 20 ; GLY(S)-GLU(S)-LYS(C)
66 68 71 2 127 20 ; GLU(S)-LYS(C)-ALA(C)
68 71 72 2 127 20 ; LYS(C)-ALA(C)-LYS(C)
71 72 75 2 127 20 ; ALA(C)-LYS(C)-ASP(S)
72 75 77 2 127 20 ; LYS(C)-ASP(S)-TYR(S)
75 77 81 2 130 20 ; ASP(S)-TYR(S)-VAL(S)
77 81 83 2 130 20 ; TYR(S)-VAL(S)-VAL(S)
81 83 85 2 127 20 ; VAL(S)-VAL(S)-GLU(C)
83 85 87 2 127 20 ; VAL(S)-GLU(C)-LYS(C)
85 87 90 2 127 20 ; GLU(C)-LYS(C)-ASN(S)
87 90 92 2 127 20 ; LYS(C)-ASN(S)-SER(S)
90 92 94 2 130 20 ; ASN(S)-SER(S)-GLU(S)
92 94 96 2 127 20 ; SER(S)-GLU(S)-THR(C)
94 96 98 2 127 20 ; GLU(S)-THR(C)-ALA(C)
96 98 99 2 100 20 ; THR(C)-ALA(C)-ASP(T)
98 99 101 2 100 20 ; ALA(C)-ASP(T)-THR(1)
99 101 103 2 100 20 ; ASP(T)-THR(1)-LEU(1)
101 103 105 2 96 700 ; THR(1)-LEU(1)-GLY(1)
103 105 106 2 96 700 ; LEU(1)-GLY(1)-LYS(1)
105 106 109 2 96 700 ; GLY(1)-LYS(1)-GLU(H)
106 109 111 2 96 700 ; LYS(1)-GLU(H)-ALA(H)
109 111 112 2 96 700 ; GLU(H)-ALA(H)-GLU(H)
111 112 114 2 96 700 ; ALA(H)-GLU(H)-LYS(H)
112 114 117 2 96 700 ; GLU(H)-LYS(H)-ALA(H)
114 117 118 2 96 700 ; LYS(H)-ALA(H)-ALA(2)
117 118 119 2 96 700 ; ALA(H)-ALA(2)-ALA(2)
118 119 120 2 96 700 ; ALA(2)-ALA(2)-TYR(2)
119 120 124 2 96 700 ; ALA(2)-TYR(2)-VAL(2)
120 124 126 2 100 20 ; TYR(2)-VAL(2)-GLU(T)
124 126 128 2 100 20 ; VAL(2)-GLU(T)-GLU(1)
126 128 130 2 100 20 ; GLU(T)-GLU(1)-LYS(1)
128 130 133 2 96 700 ; GLU(1)-LYS(1)-GLY(1)
130 133 134 2 96 700 ; LYS(1)-GLY(1)-LYS(1)
133 134 137 2 96 700 ; GLY(1)-LYS(1)-GLU(H)
134 137 139 2 96 700 ; LYS(1)-GLU(H)-ALA(H)
137 139 140 2 96 700 ; GLU(H)-ALA(H)-ALA(H)
139 140 141 2 96 700 ; ALA(H)-ALA(H)-ASN(H)
140 141 143 2 96 700 ; ALA(H)-ASN(H)-LYS(2)
141 143 146 2 96 700 ; ASN(H)-LYS(2)-ALA(2)
143 146 147 2 96 700 ; LYS(2)-ALA(2)-ALA(2)
146 147 148 2 96 700 ; ALA(2)-ALA(2)-GLU(2)
147 148 150 2 100 20 ; ALA(2)-GLU(2)-PHE(T)
148 150 154 2 100 20 ; GLU(2)-PHE(T)-ALA(T)
150 154 155 2 100 20 ; PHE(T)-ALA(T)-GLU(3)
154 155 157 2 100 20 ; ALA(T)-GLU(3)-GLY(3)
155 157 158 2 96 700 ; GLU(3)-GLY(3)-LYS(3)
157 158 161 2 96 700 ; GLY(3)-LYS(3)-ALA(3)
158 161 162 2 127 20 ; LYS(3)-ALA(3)-GLY(C)
161 162 163 2 127 20 ; ALA(3)-GLY(C)-GLU(C)
162 163 165 2 127 20 ; GLY(C)-GLU(C)-ALA(S)
163 165 166 2 127 20 ; GLU(C)-ALA(S)-LYS(S)
165 166 169 2 130 20 ; ALA(S)-LYS(S)-ASP(S)
166 169 171 2 127 20 ; LYS(S)-ASP(S)-ALA(C)
169 171 172 2 127 20 ; ASP(S)-ALA(C)-THR(C)
171 172 174 2 127 20 ; ALA(C)-THR(C)-LYS(C)
; Backbone-sidechain angles
1 2 3 2 100 25 ; ALA(C)-LYS(C) SBB
5 6 7 2 100 25 ; GLY(S)-ASP(1) SBB
8 9 10 2 100 25 ; GLY(3)-ASN(3) SBB
9 11 12 2 100 25 ; ASN(3)-ILE(3) SBB
11 13 14 2 100 25 ; ILE(3)-LEU(2) SBB
13 15 16 2 100 25 ; LEU(2)-ASP(T) SBB
15 17 18 2 100 25 ; ASP(T)-ASP(1) SBB
17 19 20 2 100 25 ; ASP(1)-LEU(1) SBB
19 21 22 2 100 25 ; LEU(1)-ASN(1) SBB
21 23 24 2 100 25 ; ASN(1)-GLU(1) SBB
25 26 27 2 100 25 ; ALA(H)-THR(H) SBB
26 28 29 2 100 25 ; THR(H)-LYS(H) SBB
28 31 32 2 100 25 ; LYS(H)-LYS(H) SBB
34 35 36 2 100 25 ; ALA(H)-SER(H) SBB
35 37 38 2 100 25 ; SER(H)-ASP(H) SBB
37 39 40 2 100 25 ; ASP(H)-PHE(H) SBB
39 43 44 2 100 25 ; PHE(H)-VAL(H) SBB
43 45 46 2 100 25 ; VAL(H)-THR(H) SBB
45 47 48 2 100 25 ; THR(H)-ASP(H) SBB
47 49 50 2 100 25 ; ASP(H)-LYS(H) SBB
49 52 53 2 100 25 ; LYS(H)-THR(H) SBB
52 54 55 2 100 25 ; THR(H)-LYS(2) SBB
54 57 58 2 100 25 ; LYS(2)-GLU(2) SBB
59 60 61 2 100 25 ; ALA(2)-LEU(2) SBB
62 63 64 2 100 25 ; ALA(S)-ASP(C) SBB
65 66 67 2 100 25 ; GLY(S)-GLU(S) SBB
66 68 69 2 100 25 ; GLU(S)-LYS(C) SBB
71 72 73 2 100 25 ; ALA(C)-LYS(C) SBB
72 75 76 2 100 25 ; LYS(C)-ASP(S) SBB
75 77 78 2 100 25 ; ASP(S)-TYR(S) SBB
77 81 82 2 100 25 ; TYR(S)-VAL(S) SBB
81 83 84 2 100 25 ; VAL(S)-VAL(S) SBB
83 85 86 2 100 25 ; VAL(S)-GLU(C) SBB
85 87 88 2 100 25 ; GLU(C)-LYS(C) SBB
87 90 91 2 100 25 ; LYS(C)-ASN(S) SBB
90 92 93 2 100 25 ; ASN(S)-SER(S) SBB
92 94 95 2 100 25 ; SER(S)-GLU(S) SBB
94 96 97 2 100 25 ; GLU(S)-THR(C) SBB
98 99 100 2 100 25 ; ALA(C)-ASP(T) SBB
99 101 102 2 100 25 ; ASP(T)-THR(1) SBB
101 103 104 2 100 25 ; THR(1)-LEU(1) SBB
105 106 107 2 100 25 ; GLY(1)-LYS(1) SBB
106 109 110 2 100 25 ; LYS(1)-GLU(H) SBB
111 112 113 2 100 25 ; ALA(H)-GLU(H) SBB
112 114 115 2 100 25 ; GLU(H)-LYS(H) SBB
119 120 121 2 100 25 ; ALA(2)-TYR(2) SBB
120 124 125 2 100 25 ; TYR(2)-VAL(2) SBB
124 126 127 2 100 25 ; VAL(2)-GLU(T) SBB
126 128 129 2 100 25 ; GLU(T)-GLU(1) SBB
128 130 131 2 100 25 ; GLU(1)-LYS(1) SBB
133 134 135 2 100 25 ; GLY(1)-LYS(1) SBB
134 137 138 2 100 25 ; LYS(1)-GLU(H) SBB
140 141 142 2 100 25 ; ALA(H)-ASN(H) SBB
141 143 144 2 100 25 ; ASN(H)-LYS(2) SBB
147 148 149 2 100 25 ; ALA(2)-GLU(2) SBB
148 150 151 2 100 25 ; GLU(2)-PHE(T) SBB
154 155 156 2 100 25 ; ALA(T)-GLU(3) SBB
157 158 159 2 100 25 ; GLY(3)-LYS(3) SBB
162 163 164 2 100 25 ; GLY(C)-GLU(C) SBB
165 166 167 2 100 25 ; ALA(S)-LYS(S) SBB
166 169 170 2 100 25 ; LYS(S)-ASP(S) SBB
171 172 173 2 100 25 ; ALA(C)-THR(C) SBB
172 174 175 2 100 25 ; THR(C)-LYS(C) SBB
; Sidechain angles
2 3 4 2 180 25 ; LYS
28 29 30 2 180 25 ; LYS
31 32 33 2 180 25 ; LYS
39 40 41 2 150 50 ; PHE
39 40 42 2 150 50 ; PHE
49 50 51 2 180 25 ; LYS
54 55 56 2 180 25 ; LYS
68 69 70 2 180 25 ; LYS
72 73 74 2 180 25 ; LYS
77 78 79 2 150 50 ; TYR
77 78 80 2 150 50 ; TYR
87 88 89 2 180 25 ; LYS
106 107 108 2 180 25 ; LYS
114 115 116 2 180 25 ; LYS
120 121 122 2 150 50 ; TYR
120 121 123 2 150 50 ; TYR
130 131 132 2 180 25 ; LYS
134 135 136 2 180 25 ; LYS
143 144 145 2 180 25 ; LYS
150 151 152 2 150 50 ; PHE
150 151 153 2 150 50 ; PHE
158 159 160 2 180 25 ; LYS
166 167 168 2 180 25 ; LYS
174 175 176 2 180 25 ; LYS
[ dihedrals ]
; Backbone dihedrals
6 8 9 11 1 -120 400 1 ; ASP(1)-GLY(3)-ASN(3)-ILE(3)
8 9 11 13 1 -120 400 1 ; GLY(3)-ASN(3)-ILE(3)-LEU(2)
17 19 21 23 1 -120 400 1 ; ASP(1)-LEU(1)-ASN(1)-GLU(1)
19 21 23 25 1 -120 400 1 ; LEU(1)-ASN(1)-GLU(1)-ALA(H)
21 23 25 26 1 -120 400 1 ; ASN(1)-GLU(1)-ALA(H)-THR(H)
23 25 26 28 1 -120 400 1 ; GLU(1)-ALA(H)-THR(H)-LYS(H)
25 26 28 31 1 -120 400 1 ; ALA(H)-THR(H)-LYS(H)-LYS(H)
26 28 31 34 1 -120 400 1 ; THR(H)-LYS(H)-LYS(H)-ALA(H)
28 31 34 35 1 -120 400 1 ; LYS(H)-LYS(H)-ALA(H)-SER(H)
31 34 35 37 1 -120 400 1 ; LYS(H)-ALA(H)-SER(H)-ASP(H)
34 35 37 39 1 -120 400 1 ; ALA(H)-SER(H)-ASP(H)-PHE(H)
35 37 39 43 1 -120 400 1 ; SER(H)-ASP(H)-PHE(H)-VAL(H)
37 39 43 45 1 -120 400 1 ; ASP(H)-PHE(H)-VAL(H)-THR(H)
39 43 45 47 1 -120 400 1 ; PHE(H)-VAL(H)-THR(H)-ASP(H)
43 45 47 49 1 -120 400 1 ; VAL(H)-THR(H)-ASP(H)-LYS(H)
45 47 49 52 1 -120 400 1 ; THR(H)-ASP(H)-LYS(H)-THR(H)
47 49 52 54 1 -120 400 1 ; ASP(H)-LYS(H)-THR(H)-LYS(2)
49 52 54 57 1 -120 400 1 ; LYS(H)-THR(H)-LYS(2)-GLU(2)
52 54 57 59 1 -120 400 1 ; THR(H)-LYS(2)-GLU(2)-ALA(2)
54 57 59 60 1 -120 400 1 ; LYS(2)-GLU(2)-ALA(2)-LEU(2)
101 103 105 106 1 -120 400 1 ; THR(1)-LEU(1)-GLY(1)-LYS(1)
103 105 106 109 1 -120 400 1 ; LEU(1)-GLY(1)-LYS(1)-GLU(H)
105 106 109 111 1 -120 400 1 ; GLY(1)-LYS(1)-GLU(H)-ALA(H)
106 109 111 112 1 -120 400 1 ; LYS(1)-GLU(H)-ALA(H)-GLU(H)
109 111 112 114 1 -120 400 1 ; GLU(H)-ALA(H)-GLU(H)-LYS(H)
111 112 114 117 1 -120 400 1 ; ALA(H)-GLU(H)-LYS(H)-ALA(H)
112 114 117 118 1 -120 400 1 ; GLU(H)-LYS(H)-ALA(H)-ALA(2)
114 117 118 119 1 -120 400 1 ; LYS(H)-ALA(H)-ALA(2)-ALA(2)
117 118 119 120 1 -120 400 1 ; ALA(H)-ALA(2)-ALA(2)-TYR(2)
118 119 120 124 1 -120 400 1 ; ALA(2)-ALA(2)-TYR(2)-VAL(2)
128 130 133 134 1 -120 400 1 ; GLU(1)-LYS(1)-GLY(1)-LYS(1)
130 133 134 137 1 -120 400 1 ; LYS(1)-GLY(1)-LYS(1)-GLU(H)
133 134 137 139 1 -120 400 1 ; GLY(1)-LYS(1)-GLU(H)-ALA(H)
134 137 139 140 1 -120 400 1 ; LYS(1)-GLU(H)-ALA(H)-ALA(H)
137 139 140 141 1 -120 400 1 ; GLU(H)-ALA(H)-ALA(H)-ASN(H)
139 140 141 143 1 -120 400 1 ; ALA(H)-ALA(H)-ASN(H)-LYS(2)
140 141 143 146 1 -120 400 1 ; ALA(H)-ASN(H)-LYS(2)-ALA(2)
141 143 146 147 1 -120 400 1 ; ASN(H)-LYS(2)-ALA(2)-ALA(2)
143 146 147 148 1 -120 400 1 ; LYS(2)-ALA(2)-ALA(2)-GLU(2)
155 157 158 161 1 -120 400 1 ; GLU(3)-GLY(3)-LYS(3)-ALA(3)
; Sidechain improper dihedrals
39 41 42 40 2 0 50 ; PHE
77 79 80 78 2 0 50 ; TYR
120 122 123 121 2 0 50 ; TYR
150 152 153 151 2 0 50 ; PHE
#ifdef POSRES
#ifndef POSRES_FC
#define POSRES_FC 1000.00
#endif
[ position_restraints ]
1 1 POSRES_FC POSRES_FC POSRES_FC
2 1 POSRES_FC POSRES_FC POSRES_FC
5 1 POSRES_FC POSRES_FC POSRES_FC
6 1 POSRES_FC POSRES_FC POSRES_FC
8 1 POSRES_FC POSRES_FC POSRES_FC
9 1 POSRES_FC POSRES_FC POSRES_FC
11 1 POSRES_FC POSRES_FC POSRES_FC
13 1 POSRES_FC POSRES_FC POSRES_FC
15 1 POSRES_FC POSRES_FC POSRES_FC
17 1 POSRES_FC POSRES_FC POSRES_FC
19 1 POSRES_FC POSRES_FC POSRES_FC
21 1 POSRES_FC POSRES_FC POSRES_FC
23 1 POSRES_FC POSRES_FC POSRES_FC
25 1 POSRES_FC POSRES_FC POSRES_FC
26 1 POSRES_FC POSRES_FC POSRES_FC
28 1 POSRES_FC POSRES_FC POSRES_FC
31 1 POSRES_FC POSRES_FC POSRES_FC
34 1 POSRES_FC POSRES_FC POSRES_FC
35 1 POSRES_FC POSRES_FC POSRES_FC
37 1 POSRES_FC POSRES_FC POSRES_FC
39 1 POSRES_FC POSRES_FC POSRES_FC
43 1 POSRES_FC POSRES_FC POSRES_FC
45 1 POSRES_FC POSRES_FC POSRES_FC
47 1 POSRES_FC POSRES_FC POSRES_FC
49 1 POSRES_FC POSRES_FC POSRES_FC
52 1 POSRES_FC POSRES_FC POSRES_FC
54 1 POSRES_FC POSRES_FC POSRES_FC
57 1 POSRES_FC POSRES_FC POSRES_FC
59 1 POSRES_FC POSRES_FC POSRES_FC
60 1 POSRES_FC POSRES_FC POSRES_FC
62 1 POSRES_FC POSRES_FC POSRES_FC
63 1 POSRES_FC POSRES_FC POSRES_FC
65 1 POSRES_FC POSRES_FC POSRES_FC
66 1 POSRES_FC POSRES_FC POSRES_FC
68 1 POSRES_FC POSRES_FC POSRES_FC
71 1 POSRES_FC POSRES_FC POSRES_FC
72 1 POSRES_FC POSRES_FC POSRES_FC
75 1 POSRES_FC POSRES_FC POSRES_FC
77 1 POSRES_FC POSRES_FC POSRES_FC
81 1 POSRES_FC POSRES_FC POSRES_FC
83 1 POSRES_FC POSRES_FC POSRES_FC
85 1 POSRES_FC POSRES_FC POSRES_FC
87 1 POSRES_FC POSRES_FC POSRES_FC
90 1 POSRES_FC POSRES_FC POSRES_FC
92 1 POSRES_FC POSRES_FC POSRES_FC
94 1 POSRES_FC POSRES_FC POSRES_FC
96 1 POSRES_FC POSRES_FC POSRES_FC
98 1 POSRES_FC POSRES_FC POSRES_FC
99 1 POSRES_FC POSRES_FC POSRES_FC
101 1 POSRES_FC POSRES_FC POSRES_FC
103 1 POSRES_FC POSRES_FC POSRES_FC
105 1 POSRES_FC POSRES_FC POSRES_FC
106 1 POSRES_FC POSRES_FC POSRES_FC
109 1 POSRES_FC POSRES_FC POSRES_FC
111 1 POSRES_FC POSRES_FC POSRES_FC
112 1 POSRES_FC POSRES_FC POSRES_FC
114 1 POSRES_FC POSRES_FC POSRES_FC
117 1 POSRES_FC POSRES_FC POSRES_FC
118 1 POSRES_FC POSRES_FC POSRES_FC
119 1 POSRES_FC POSRES_FC POSRES_FC
120 1 POSRES_FC POSRES_FC POSRES_FC
124 1 POSRES_FC POSRES_FC POSRES_FC
126 1 POSRES_FC POSRES_FC POSRES_FC
128 1 POSRES_FC POSRES_FC POSRES_FC
130 1 POSRES_FC POSRES_FC POSRES_FC
133 1 POSRES_FC POSRES_FC POSRES_FC
134 1 POSRES_FC POSRES_FC POSRES_FC
137 1 POSRES_FC POSRES_FC POSRES_FC
139 1 POSRES_FC POSRES_FC POSRES_FC
140 1 POSRES_FC POSRES_FC POSRES_FC
141 1 POSRES_FC POSRES_FC POSRES_FC
143 1 POSRES_FC POSRES_FC POSRES_FC
146 1 POSRES_FC POSRES_FC POSRES_FC
147 1 POSRES_FC POSRES_FC POSRES_FC
148 1 POSRES_FC POSRES_FC POSRES_FC
150 1 POSRES_FC POSRES_FC POSRES_FC
154 1 POSRES_FC POSRES_FC POSRES_FC
155 1 POSRES_FC POSRES_FC POSRES_FC
157 1 POSRES_FC POSRES_FC POSRES_FC
158 1 POSRES_FC POSRES_FC POSRES_FC
161 1 POSRES_FC POSRES_FC POSRES_FC
162 1 POSRES_FC POSRES_FC POSRES_FC
163 1 POSRES_FC POSRES_FC POSRES_FC
165 1 POSRES_FC POSRES_FC POSRES_FC
166 1 POSRES_FC POSRES_FC POSRES_FC
169 1 POSRES_FC POSRES_FC POSRES_FC
171 1 POSRES_FC POSRES_FC POSRES_FC
172 1 POSRES_FC POSRES_FC POSRES_FC
174 1 POSRES_FC POSRES_FC POSRES_FC
One more thin that i forgot to mention before.
At the beginning of the simulation i got several warnings regarding the system pressure:
10000000 steps, 100000.0 ps.
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
Step 1 Warning: pressure scaling more than 1%, mu: 0.977723 0.977723 0.981853
NOTE: Turning on dynamic load balancing
Are this warnings something to worry about?And if they are, what can i do to fix the problem?
Thanks again Floris for your help.
Best,
Carlos
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- mnmelo
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The pressure fluctuations are normal in the initial equilibration steps of insane systems, which start quite far from equilibrium.
Regarding your protein freezing, and in addition to Floris' checks:
I'm assuming that other than the temperature both systems are the same.
Can you check if the water itself isn't frozen? Martini water freezes at somewhat hotter temperatures than the real thing, though most of the times one can get away with that since crystals fail to nucleate and systems remain happily fluid.
In your system you're not giving your molecules any initial temperature kick. This may help water crystals nucleate and grow on the protein or membrane surfaces, and before you know it you have a nice frozen water phase.
If freezing is indeed affecting your system it might also be useful to remove the bilayer's and the water phase's COM motion separately (read up on the 'flying ice cube effect'). Just split your system into two index groups 'Solvent' and 'Bilayer', and set 'comm-grps = Solvent Bilayer'. (Be sure, then, to put the protein in the appropriate group: 'Solvent' if it's in the aqueous phase, 'Bilayer' if it is embedded).
Cheers, and let me know.
Manel
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- Navarro
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Thanks for the reply (and for the good advice!!)
Indeed the water beads were froze during the simulations (as well as some head groups of the Bilayer)!
What about if the protein start on the water surface, but i'm studying how the protein interact peripherally with respect to the headgroups of the membrane during the MD simulations?
I just run a test (100ns) using the following line in the *mdp file:
comm-grps = Protein Lipids W_NA
What do you think about this configuration?
One more thing.
Since I have already run several simulations at higher temperature (328K), and i found that the protein, as well as the lipids 'behaves normally', should i have to run again these systems, adding in the *mdp the comm-grps line?
Thanks for your help Manuel,
Best,
Carlos
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- mnmelo
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Now, the most obvious solution -- which I failed to mention -- is to add the so-called 'antifreeze' water particles (molecule name 'WF' in the martini itp). These are waters with a slightly larger radius that break the packing and prevent solidification. You should replace about 10% of your waters with these.
Regarding the need for separate COM motion removal:
You say your protein adsorbs onto the headgroups. I'd say this is probably enough that you don't have to worry, unless you see the protein sliding on the surface dragged by the aqueous phase. If you're studying the system from a point where the proteins starts out away from the membrane, then you might consider separately removing COM motions at least until the protein lands on the bilayer.
Here's why:
The potential problem when the COM motion is globally removed is that the phases might start sliding relative to each other while the global COM stays the same. The respective thermostats will see this translation as an increase in temperature and proceed to scale velocities down. However, this downscaling happens on all d.o.f., not only the phase translation one. The result is that heat (velocity) will effectively build up in that translational d.o.f., while the rest of the phase's d.o.f become frozen (a flying ice cube).
This problem is averted if there is effective momentum transfer between phases. A bilayer on its own will slide relatively easily through an aqueous phase. If, however, it has an embedded protein sticking out, this protein will couple both phases' movements and the ice-cube-effect is then probably negligible.
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- Navarro
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So you recommend me to set up my systems at 300K with the COM removal for the entire simulations, right?
I'll have to start reading /studying about the "flying ice cube" effect ASAP.
Best,
Carlos
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- mnmelo
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And yes, it might be good to remove COM motion separately, especially since you're interested in the temperature effect, and the consequence of the flying ice cube is a sort of misreported temperature.
Manel
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- Navarro
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I was able to run several simulations at 300K (DFMG-POPC, FPMG-POPC, OPMG-POPC, DPMG-POPC, pure DPMG and OPMG without protein) but I'm stuck simulating pure DFMG (all the system are in a cubic simulating box of 10x10x10).
For some reason, during the simulations the X and Y axys start to shrink, getting different types of error messages, like:
Step 7149080: The domain decomposition grid has shifted too much in the Y-direction around cell 1 3 0. This should not have happened. Running with fewer ranks might avoid this issue.
For more information and tips for troubleshooting, please check the GROMACS
or
The X-size of the box times the triclinic skew factor (1.000000) is smaller than the number of DD cells (4) times the smallest allowed cell size (1.800000)
This is the *mdp i'm using for all systems:
dt = 0.01
nsteps = 200000000
nstcomm = 10
comm-grps = Lipids Solvent
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 10000
nstenergy = 1000
nstxtcout = 10000
xtc_precision = 100
xtc-grps =
energygrps = Lipids Solvent
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
cutoff-scheme = group
coulombtype = Shift ;Reaction_field (for use with Verlet-pairlist) ;PME (especially with polarizable water)
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
vdw_type = Shift ;cutoff (for use with Verlet-pairlist)
rvdw_switch = 0.9
rvdw = 1.2 ;1.1 (for use with Verlet-pairlist)
tcoupl = Berendsen
tc-grps = Lipids Solvent
tau_t = 2.0 2.0
ref_t = 300 300
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 1.0 1.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0
gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30
I tried launching the simulations with 32, 16 and 8 cores, without luck :/
What could be the reason for this strange behaviour?
Best,
Carlos
edit- For some reason i cannot copy the whole content of my input *gro file, so here is it of you need to check it:
cl.ly/0X042k0S0A3K
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- mnmelo
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My bet is that you need a larger tau-p (or a lower compressibility). I'd try a tau-p of 5ps, or a traditional compressibility of 4.5e-5.
If this still fails and you keep consistently getting errors a bruteforce way to debug this and other problems is to output every step of a simulation (nstxout=1). The idea is to get a full frame trajectory leading up to the crash, and then trying to see what causes it. You must run it only for a couple thousand steps at a time (use -maxh 0.05, or similar), clean up, and then continue if it hasn't crashed yet (use -cpi and -noappend) otherwise you'll quickly create a LOT of useless trajectory data.
Other things I'd do, unrelated to solving the problem:
-Increase the dt to 0.02. This might even make the system more unstable, but Martini stuff should be able to run at dt=0.02ps, except for some special cases. (Unless, of course, you are simulating something special).
-Set nstcomm to, at least 100. I think grompp does it for you. The point is you don't need to burden the engine with comm removal so frequently.
Good luck,
Manel
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- Navarro
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Thanks for the quick reply :)
I'll try your 2 suggestions ASAP.
But i do have another questions. Considering i'll change the taup and/or compressibility for just one simulation, this change will no altere a future proper comparison with the other simulations?
Thanks again!
Carlos
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- mnmelo
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On the other hand, since that crash happened well into 70ns of simulation, it might just be some rare instability. If you rerun the simulation with the same parameters you might get it to finish cleanly.
Manel
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- Navarro
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I tried reruning the simulations several times with the same issues. The only difference, it that they crashed at different times, but non of them has passed at least the 100ns.
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- mnmelo
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If you do get the dt=0.02 to work, it's already half the simulating you'll have to do. (don't forget to double the trajectory and energy output frequencies, then. Forgot to mention that earlier).
Manel
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