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Problem in minimizing protein/bilayer system
- abhinavsri89
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2 years 3 months ago #9275
by abhinavsri89
Problem in minimizing protein/bilayer system was created by abhinavsri89
Hi Martini Users,
I am trying to run a CG simulation for a protein bilayer system.
Following are the steps which I opted:
1). Converting the all atom structure of protein to CG structure using the following
python3 martinize.py -f 7kjr.pdb -o PROTEIN-TOPOLOGY.top -x 7kjr-CG.pdb -dssp /usr/bin/mkdssp -p backbone -ff martini22
2). Generating the protein/bilayer/cholesterol system using the following
python2 insane.py -f 7kjr-CG.pdb -l DPPC:1 -l DIPC:1 -l CHOL:1 -sol W -ring -d 5 -dz 10 -dm -12 -o SARS-COV-2-RES-BILAYER-SYSTEM.gro -p SARS-COV-2-RES-BILAYER-SYSTEM.top
When I try to run simulation using martini mdp file, I get the following error:
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 8 atoms. The longest distance involved in such interactions is
9.153 nm which is above half the box length. This molecule type consists of
muliple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.
Following is the martini mdp file parameters which I am using
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.
title = Martini
; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.
integrator = md
dt = 0.002
nsteps = 60000000
nstcomm = 100
comm-grps =
;nstxout = 25000
;nstvout = 10000
;nstfout = 10000
nstlog = 1000
nstenergy = 10000
nstxout-compressed = 5000
compressed-x-precision = 100
compressed-x-grps =
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = force-switch
rvdw = 1.2
tcoupl = v-rescale
tc-grps = DPPC W CHOL DIPC Protein
tau_t = 1.0 1.0 1.0 1.0 1.0
ref_t = 295 295 295 295 295
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4 3e-4 3e-4 3e-4
ref_p = 1.0 1.0 1.0 1.0 1.0
refcoord-scaling = All
gen_vel = no
gen_temp = 295
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
It will be very great if anyone can help.
Thanks in advance !
- Abhinav Srivastava
I am trying to run a CG simulation for a protein bilayer system.
Following are the steps which I opted:
1). Converting the all atom structure of protein to CG structure using the following
python3 martinize.py -f 7kjr.pdb -o PROTEIN-TOPOLOGY.top -x 7kjr-CG.pdb -dssp /usr/bin/mkdssp -p backbone -ff martini22
2). Generating the protein/bilayer/cholesterol system using the following
python2 insane.py -f 7kjr-CG.pdb -l DPPC:1 -l DIPC:1 -l CHOL:1 -sol W -ring -d 5 -dz 10 -dm -12 -o SARS-COV-2-RES-BILAYER-SYSTEM.gro -p SARS-COV-2-RES-BILAYER-SYSTEM.top
When I try to run simulation using martini mdp file, I get the following error:
Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 8 atoms. The longest distance involved in such interactions is
9.153 nm which is above half the box length. This molecule type consists of
muliple parts, e.g. monomers, that are connected by interactions that are not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.
Following is the martini mdp file parameters which I am using
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.x
; Updated 15 Jul 2015 by DdJ
;
; for use with GROMACS 5
; For a thorough comparison of different mdp options in combination with the Martini force field, see:
; D.H. de Jong et al., Martini straight: boosting performance using a shorter cutoff and GPUs, submitted.
title = Martini
; TIMESTEP IN MARTINI
; Most simulations are numerically stable with dt=40 fs,
; however better energy conservation is achieved using a
; 20-30 fs timestep.
; Time steps smaller than 20 fs are not required unless specifically stated in the itp file.
integrator = md
dt = 0.002
nsteps = 60000000
nstcomm = 100
comm-grps =
;nstxout = 25000
;nstvout = 10000
;nstfout = 10000
nstlog = 1000
nstenergy = 10000
nstxout-compressed = 5000
compressed-x-precision = 100
compressed-x-grps =
cutoff-scheme = Verlet
nstlist = 20
ns_type = grid
pbc = xyz
verlet-buffer-tolerance = 0.005
coulombtype = reaction-field
rcoulomb = 1.2
epsilon_r = 15 ; 2.5 (with polarizable water)
epsilon_rf = 0
vdw_type = cutoff
vdw-modifier = force-switch
rvdw = 1.2
tcoupl = v-rescale
tc-grps = DPPC W CHOL DIPC Protein
tau_t = 1.0 1.0 1.0 1.0 1.0
ref_t = 295 295 295 295 295
Pcoupl = Berendsen
Pcoupltype = semiisotropic
tau_p = 12.0 ;parrinello-rahman is more stable with larger tau-p, DdJ, 20130422
compressibility = 3e-4 3e-4 3e-4 3e-4 3e-4
ref_p = 1.0 1.0 1.0 1.0 1.0
refcoord-scaling = All
gen_vel = no
gen_temp = 295
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
It will be very great if anyone can help.
Thanks in advance !
- Abhinav Srivastava
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