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amino acid bonds
- yamahdi
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13 years 3 months ago #459
by yamahdi
amino acid bonds was created by yamahdi
Hi every body
as I have understood the bonds between beads of following amino acids THR, VAL, ILE,are different from the others and are weaker. I think the root of linc warning mentioned in my previous question may be here. would you pleaes help me?
thanks for your kind help in advance
as I have understood the bonds between beads of following amino acids THR, VAL, ILE,are different from the others and are weaker. I think the root of linc warning mentioned in my previous question may be here. would you pleaes help me?
thanks for your kind help in advance
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- xavier
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13 years 3 months ago #461
by xavier
Replied by xavier on topic amino acid bonds
As a matter of fact the distribution of the bond between the backbone and the side chains of the residues you mention are so narrow that it was decided to describe them with constraints instead of regular bonds, in which case it would have been necessary to use a very (too) high force constant.
This basically means that the bonds are "strong" and I am not sure how that relates to the lincs warnings!
XAvier.
This basically means that the bonds are "strong" and I am not sure how that relates to the lincs warnings!
XAvier.
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- yamahdi
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13 years 3 months ago #462
by yamahdi
Replied by yamahdi on topic amino acid bonds
Hi,
now where may has been my mistake resulting in LINCS WARNING in first step of in vacuum simulation of some proteins?!!!
as I have see the error is about over load and pressure in beads of Val, THR and Ile leading in big changes in angles and...!
thanks from your kind help in advance
now where may has been my mistake resulting in LINCS WARNING in first step of in vacuum simulation of some proteins?!!!
as I have see the error is about over load and pressure in beads of Val, THR and Ile leading in big changes in angles and...!
thanks from your kind help in advance
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13 years 3 months ago #463
by xavier
Replied by xavier on topic amino acid bonds
To make sure we talk about the same thing:
you experience lincs warnings during minimization of your CG protein!
One question: does the minimization gets to completion?
It is probable that your starting structure contains some bad contact resulting in strong forces ... did you check for such bad contact?
It might be good that you describe your protocol in more details
XAvier.
you experience lincs warnings during minimization of your CG protein!
One question: does the minimization gets to completion?
It is probable that your starting structure contains some bad contact resulting in strong forces ... did you check for such bad contact?
It might be good that you describe your protocol in more details
XAvier.
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13 years 3 months ago #464
by yamahdi
Replied by yamahdi on topic amino acid bonds
1- minimization doesn't get to completion!
2- it seems VMD doesn't show any bad contact!
3- the beads at which warning error has been seen are exactly the beads of VAL, THR, ILE.
4- We exactly have done the steps of toturial at your site and have used the seq2itp and so ... which are located at the web.
thanks
2- it seems VMD doesn't show any bad contact!
3- the beads at which warning error has been seen are exactly the beads of VAL, THR, ILE.
4- We exactly have done the steps of toturial at your site and have used the seq2itp and so ... which are located at the web.
thanks
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- xavier
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13 years 3 months ago #465
by xavier
Replied by xavier on topic amino acid bonds
Ok in that case the only and most likely is that the structure file you are using is corrupted in some way.
Try to visualize both atomistic and CG pdb/gro files and make sure that all atoms are present and that nothing funky happens during the conversion. It does not make much sense that the minimization does not go through ...
XAvier.
Try to visualize both atomistic and CG pdb/gro files and make sure that all atoms are present and that nothing funky happens during the conversion. It does not make much sense that the minimization does not go through ...
XAvier.
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13 years 3 months ago #466
by siewert
Replied by siewert on topic amino acid bonds
If the starting configuration is not so good, one should not use constraints while doing minimization; this often leads to LINCS errors. The VAL, THR, and ILE side chains are the ones that are standard defined as contrained, and may give you problems during minimization.
Therefore, during minimization, it is better to convert the constraints to harmonic bonds, even when they are stiff. Once you continue with MD, you should switch back to constraints again unless you want to use a small time step.
It is all described in the FAQ, under problems 'my simulations keep crashing ...'
Therefore, during minimization, it is better to convert the constraints to harmonic bonds, even when they are stiff. Once you continue with MD, you should switch back to constraints again unless you want to use a small time step.
It is all described in the FAQ, under problems 'my simulations keep crashing ...'
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- yamahdi
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13 years 3 months ago #471
by yamahdi
Replied by yamahdi on topic amino acid bonds
Hi
we successed to have a simulation after removing constrains. then short minmization step has been done and also a short MD. but we have a problem with 2 LYS amino acids which have been separated from the model and are observed in a far distance.
there is also one question which I am not sure if have any effect on the simulation or not: for desulfide bonds as 'i have been understood, you have only presented bond's lenght and strenght and noting has been mentioned about dihedrals or angle of bond. Is it OK or there is some point I have missed?!
would you pleaes help me where may mistake?
thanks in advance
we successed to have a simulation after removing constrains. then short minmization step has been done and also a short MD. but we have a problem with 2 LYS amino acids which have been separated from the model and are observed in a far distance.
there is also one question which I am not sure if have any effect on the simulation or not: for desulfide bonds as 'i have been understood, you have only presented bond's lenght and strenght and noting has been mentioned about dihedrals or angle of bond. Is it OK or there is some point I have missed?!
would you pleaes help me where may mistake?
thanks in advance
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13 years 3 months ago #472
by xavier
Defining a disulfide bridge in the topology as been a bond with the correct equilibrium distance and force constant is indeed fine!
Replied by xavier on topic amino acid bonds
Congratulations :))Hi
we successed to have a simulation after removing constrains. then short minmization step has been done and also a short MD.
I am not sure what you mean here. Could it simply be a periodic boundary condition effect?but we have a problem with 2 LYS amino acids which have been separated from the model and are observed in a far distance.
I do not understand what is your problem here!there is also one question which I am not sure if have any effect on the simulation or not: for desulfide bonds as 'i have been understood, you have only presented bond's lenght and strenght and noting has been mentioned about dihedrals or angle of bond. Is it OK or there is some point I have missed?!
Defining a disulfide bridge in the topology as been a bond with the correct equilibrium distance and force constant is indeed fine!
XAvierwould you please help me where may mistake?
thanks in advance
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- yamahdi
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13 years 3 months ago #473
by yamahdi
Replied by yamahdi on topic amino acid bonds
I should inform that it seems that the root of the problem has been in the selected protein gro file and now every looks well! :)
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13 years 3 months ago #474
by xavier
Replied by xavier on topic amino acid bonds
I am glad to hear that :))
Good luck for the rest.
Good luck for the rest.
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- roshanak
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7 years 2 months ago #7093
by roshanak
Replied by roshanak on topic amino acid bonds
hi
i have a similar problem in minimization step. i remove constraints from .itp file and i do a successful minimization by short time step (dt=0.001 ps ) for 1 ns.
(but i must tell that beginning energy of my system was very high in the potential energy analysis before that reachs a negative amount in minimization.)
i try to do equilibration step. when i convert the constraints to .itp file, i receive lincs warning again. i try do this step without constraints, but i receive this error:
Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
G96Angle of 2564 missing 1
Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
i search for this error and i find page of gromacs documentation about blowing up. but i don't find my solution.
can you help me?
thank you
(my system includes 5 peptide to form of pantagonal in center of dppc bilayer.)
i have a similar problem in minimization step. i remove constraints from .itp file and i do a successful minimization by short time step (dt=0.001 ps ) for 1 ns.
(but i must tell that beginning energy of my system was very high in the potential energy analysis before that reachs a negative amount in minimization.)
i try to do equilibration step. when i convert the constraints to .itp file, i receive lincs warning again. i try do this step without constraints, but i receive this error:
Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
G96Angle of 2564 missing 1
Program mdrun, VERSION 4.5.5
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
i search for this error and i find page of gromacs documentation about blowing up. but i don't find my solution.
can you help me?
thank you
(my system includes 5 peptide to form of pantagonal in center of dppc bilayer.)
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7 years 2 months ago #7096
by peterkroon
Replied by peterkroon on topic amino acid bonds
Please post the commands you issued (copy-paste, don't retype) to generate the structures and run the simulation, and your mdp file.
It seems that your starting configuration is just not good/stable enough. Check for clashing atoms.
It seems that your starting configuration is just not good/stable enough. Check for clashing atoms.
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7 years 2 months ago - 7 years 2 months ago #7099
by roshanak
Replied by roshanak on topic amino acid bonds
thanks for reply
my commands:
$ gmx editconf -f 1.pdb -princ -o ax.gro
$ gmx editconf -f ax.gro -rotate 0 90 0 -o az.gro
$ gmx editconf -f az.gro -bt cubic -center 5.7 4.036 8 -box 10 10 12 -o box1.gro (and i do it for other boxs with their cordinates)
$./martinize2.6.py -f box1.gro -o topol1.top -x box1CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22 (i do it for box2-3-4 & 5)
$ gmx editconf -f box1CG.pdb -o box1CG.gro
$ cat box1CG.gro box2CG.gro box3CG.gro box4CG.gro box5CG.gro> a5gonCG.gro
$./insane.py -f a5gonCG.gro -o aurein-dppct.gro -p topolt.top -pbc squar
e -box 10,10,12 -l DPPC -sol W -dm 0 (topolt.top includes .itp files without constraints)
$ gmx grompp -f minimization1fDPOS.mdp -c aurein-dppct.gro -p topolt.top -o minimt.tpr
$ gmx mdrun -deffnm minimt -nt 4 -v
$ gmx make_ndx -f minimt.gro -o index.ndx
$ grompp -f equilibration.mdp -c minimt.gro -p topolt.top -o equ.tpr -n in
dex.ndx
$ mdrun -deffnm equ -nt 2 -v
minimization.mdp:
;define = -DFLEXIBLE
define = -DPOSRES
integrator = steep ; Run steepest descent energy minimization algorithm
dt = 0.001
nsteps = 1250000 ; Number of steep steps to run
nstcomm = 100
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 100 ; Output frequency for energies to log file
nstenergy = 100 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =
energygrps = System
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
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)
cutoff-scheme = group
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
equilibration.mdp:
define = -DPOSRES
;define = -DFLEXIBLE
integrator = md
dt = 0.001
nsteps = 5100000
nstcomm = 100
comm-grps = Protein_DPPC W
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000 ; Output frequency for energies to log file
nstenergy = 100 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =
energygrps = Protein_DPPC W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
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)
;cutoff-scheme = group
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
tcoupl = v-rescale
tc-grps = Protein DPPC W
tau_t = 1.0 1.0 1.0
ref_t = 323 323 323
Pcoupl = berendsen ; berendsen ; parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12 ; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4 ; 3e-4
ref_p = 1.0 1.0 ; 1.0 1.0
refcoord-scaling =com
gen_vel = yes
gen_temp = 323
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
i setup my system and do minimization step in my laptop (gromacs 2016). but i make equ.tpr and run equilibration in camputer with gromacs 4.5.5 (becaue it takes a long time)
my commands:
$ gmx editconf -f 1.pdb -princ -o ax.gro
$ gmx editconf -f ax.gro -rotate 0 90 0 -o az.gro
$ gmx editconf -f az.gro -bt cubic -center 5.7 4.036 8 -box 10 10 12 -o box1.gro (and i do it for other boxs with their cordinates)
$./martinize2.6.py -f box1.gro -o topol1.top -x box1CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22 (i do it for box2-3-4 & 5)
$ gmx editconf -f box1CG.pdb -o box1CG.gro
$ cat box1CG.gro box2CG.gro box3CG.gro box4CG.gro box5CG.gro> a5gonCG.gro
$./insane.py -f a5gonCG.gro -o aurein-dppct.gro -p topolt.top -pbc squar
e -box 10,10,12 -l DPPC -sol W -dm 0 (topolt.top includes .itp files without constraints)
$ gmx grompp -f minimization1fDPOS.mdp -c aurein-dppct.gro -p topolt.top -o minimt.tpr
$ gmx mdrun -deffnm minimt -nt 4 -v
$ gmx make_ndx -f minimt.gro -o index.ndx
$ grompp -f equilibration.mdp -c minimt.gro -p topolt.top -o equ.tpr -n in
dex.ndx
$ mdrun -deffnm equ -nt 2 -v
minimization.mdp:
;define = -DFLEXIBLE
define = -DPOSRES
integrator = steep ; Run steepest descent energy minimization algorithm
dt = 0.001
nsteps = 1250000 ; Number of steep steps to run
nstcomm = 100
comm-grps =
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 100 ; Output frequency for energies to log file
nstenergy = 100 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =
energygrps = System
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
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)
cutoff-scheme = group
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
equilibration.mdp:
define = -DPOSRES
;define = -DFLEXIBLE
integrator = md
dt = 0.001
nsteps = 5100000
nstcomm = 100
comm-grps = Protein_DPPC W
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000 ; Output frequency for energies to log file
nstenergy = 100 ; Output frequency for energies to energy file
nstxtcout = 1000 ; Output frequency for .xtc file
xtc_precision = 100
xtc-grps =
energygrps = Protein_DPPC W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
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)
;cutoff-scheme = group
;coulomb-modifier = Potential-shift
;vdw-modifier = Potential-shift
;epsilon_rf = 0 ; epsilon_rf = 0 really means epsilon_rf = infinity
;verlet-buffer-drift = 0.005
tcoupl = v-rescale
tc-grps = Protein DPPC W
tau_t = 1.0 1.0 1.0
ref_t = 323 323 323
Pcoupl = berendsen ; berendsen ; parrinello-rahman
Pcoupltype = semiisotropic
tau_p = 12 ; 12.0 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4 ; 3e-4
ref_p = 1.0 1.0 ; 1.0 1.0
refcoord-scaling =com
gen_vel = yes
gen_temp = 323
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
continuation = no
lincs_order = 4
lincs_warnangle = 30
i setup my system and do minimization step in my laptop (gromacs 2016). but i make equ.tpr and run equilibration in camputer with gromacs 4.5.5 (becaue it takes a long time)
Last edit: 7 years 2 months ago by roshanak.
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- roshanak
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7 years 2 months ago #7108
by roshanak
Replied by roshanak on topic amino acid bonds
please help me :(
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- peterkroon
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7 years 2 months ago - 7 years 2 months ago #7110
by peterkroon
Replied by peterkroon on topic amino acid bonds
Few points:
1) your gromacs version is truly ancient. Do you have a good reason for not upgrading?
2) I'm not sure you need 3 different TC groups. If the protein is properly embedded in the membrane I would merge it with the lipid group, and if it's really in both solvent and membrane I would either use just 1 TC group, or 3 like you have now.
Did you check your initial structure for clashes and/or missing atoms in the protein?
And did your minimization converge? Or did it run out of steps?
1) your gromacs version is truly ancient. Do you have a good reason for not upgrading?
2) I'm not sure you need 3 different TC groups. If the protein is properly embedded in the membrane I would merge it with the lipid group, and if it's really in both solvent and membrane I would either use just 1 TC group, or 3 like you have now.
Did you check your initial structure for clashes and/or missing atoms in the protein?
And did your minimization converge? Or did it run out of steps?
Last edit: 7 years 2 months ago by peterkroon.
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7 years 2 months ago - 7 years 2 months ago #7111
by roshanak
Replied by roshanak on topic amino acid bonds
1. The computer is for our university and will be updated until a few month later :)
2. I want to study behavior of this pentagonal into the membrane. at the first, I put the peptides in center of membrane.I want to see what'll happen. Whether the water penetrates into the membrane? I thought that must be 3 group. Is it wrong?
Minimization without constraints was successful and it converged.
In my initial structure seems some lipids are very near the peptides. that seems the some lipid's beads stick to some of peptide's beads. i do this step with insane.py
thank you
2. I want to study behavior of this pentagonal into the membrane. at the first, I put the peptides in center of membrane.I want to see what'll happen. Whether the water penetrates into the membrane? I thought that must be 3 group. Is it wrong?
Minimization without constraints was successful and it converged.
In my initial structure seems some lipids are very near the peptides. that seems the some lipid's beads stick to some of peptide's beads. i do this step with insane.py
thank you
Last edit: 7 years 2 months ago by roshanak.
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7 years 2 months ago - 7 years 2 months ago #7112
by roshanak
Replied by roshanak on topic amino acid bonds
I read in other post, about increasing lincs order (from 4 to 8). is it reasonable in my case?
I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
Potential energy, temperature and pressure analysis show very very small fluctuations (almost linear). Is it normal?
I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
Potential energy, temperature and pressure analysis show very very small fluctuations (almost linear). Is it normal?
Last edit: 7 years 2 months ago by roshanak.
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7 years 2 months ago - 7 years 2 months ago #7113
by roshanak
Replied by roshanak on topic amino acid bonds
I told that lipid's bead is very near to peptide's bead in insane.py step. But just now, I look at the membrane proteins (kalp) tutorial files.That seems as close as my case.
I forget to tell that i look at the files before insane.py and after minimization, all atoms exist.
I forget to tell that i look at the files before insane.py and after minimization, all atoms exist.
Last edit: 7 years 2 months ago by roshanak.
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7 years 2 months ago #7115
by peterkroon
Replied by peterkroon on topic amino acid bonds
Are all atoms present in "1.pdb"? Especially if you got it from X-ray there may be some unresolved atoms.
Can you find for me the shortest distance between any two beads after the minimization?
>I read in other post, about increasing lincs order (from 4 to 8). is it reasonable in my case?
I might help, but the effect is more pronounced if there are a lot of constraints in your system (i.e. polarizable water)
>I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
What does this mean?
>Potential energy, temperature and pressure analysis show very very small fluctuations (almost linear). Is it normal?
Yes.
Can you find for me the shortest distance between any two beads after the minimization?
>I read in other post, about increasing lincs order (from 4 to 8). is it reasonable in my case?
I might help, but the effect is more pronounced if there are a lot of constraints in your system (i.e. polarizable water)
>I try it and equilibration was done. But i see in my structure, at the top of peptides, some NC3 beads (for 7 lipids).
What does this mean?
>Potential energy, temperature and pressure analysis show very very small fluctuations (almost linear). Is it normal?
Yes.
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