From: [email protected]
To: [email protected]
Subject: RE: [gmx-users] Position Restraints problem
Date: Thu, 15 Oct 2015 09:20:49 +0000
I'm sorry but I don't think my case is one of the phenomena described in the
list, the problem appears after applying the restraints, and not after the pbc.
Using explicit solvent method I didn't detect this problem, using the method of
implicit solvent instead the structure appears as attached.
This is the mdp file I used to apply the restraints:
; run parameters for position restraints
; with temperature and pressure equilibration
; values appropriate for CHARMM27 force field
include = -I. -I.. -I../top
define = -DPOSRES
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 12500
nstxout = 500
nstvout = 500
nstfout = 500
nstlog = 500
nstenergy = 500
comm-mode = Linear
nstcomm = 1000
comm-grps = SYSTEM
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.0
coulombtype = Cut-off
rcoulomb = 1.2
epsilon_r = 1
epsilon_rf = 54
vdw-type = Cut-off
rvdw-switch = 1.0
rvdw = 1.2
DispCorr = EnerPres
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
Tcoupl = V-rescale
tau_t = 0.1
tc-grps = protein
ref_t = 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
refcoord_scaling = COM
gen_vel = yes
gen-temp = 300
gen_seed = -1
constraints = all-bonds
constraint-algorithm = Lincs
lincs-order = 4
lincs-iter = 1
; Implicit solvent
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 0.0054
My itp file:
; i funct fcx fcy fcz
175 1 1000 1000 1000
176 1 1000 1000 1000
177 1 1000 1000 1000
178 1 1000 1000 1000
179 1 1000 1000 1000
180 1 1000 1000 1000
181 1 1000 1000 1000
182 1 1000 1000 1000
183 1 1000 1000 1000
184 1 1000 1000 1000
185 1 1000 1000 1000
186 1 1000 1000 1000
187 1 1000 1000 1000
188 1 1000 1000 1000
189 1 1000 1000 1000
190 1 1000 1000 1000
191 1 1000 1000 1000
192 1 1000 1000 1000
193 1 1000 1000 1000
194 1 1000 1000 1000
195 1 1000 1000 1000
196 1 1000 1000 1000
197 1 1000 1000 1000
198 1 1000 1000 1000
199 1 1000 1000 1000
200 1 1000 1000 1000
201 1 1000 1000 1000
202 1 1000 1000 1000
203 1 1000 1000 1000
204 1 1000 1000 1000
205 1 1000 1000 1000
206 1 1000 1000 1000
207 1 1000 1000 1000
208 1 1000 1000 1000
209 1 1000 1000 1000
210 1 1000 1000 1000
211 1 1000 1000 1000
212 1 1000 1000 1000
213 1 1000 1000 1000
214 1 1000 1000 1000
215 1 1000 1000 1000
.....etc
My top file;
Command line was:
; pdb2gmx -f 4AKE.pdb -o protein.pdb -p 4ake.top -i protein_posre.itp -ff
charmm27 -nochargegrp
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
; residue 1 MET rtp MET q +1.0
1 NH3 1 MET N 1 -0.3 14.007 ; qtot
-0.3
2 HC 1 MET H1 2 0.33 1.008 ; qtot
0.03
3 HC 1 MET H2 3 0.33 1.008 ; qtot
0.36
....etc
Include Position restraint file
#ifdef POSRES
#include "helices.itp"
#endif
[ system ]
; Name
ADENYLATE KINASE
[ molecules ]
; Compound #mols
Protein_chain_A 1
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