[gmx-users] FW: Position Restraints problem

[Chiara Bello]

From: kiarabell at msn.com
To: gmx-users at gromacs.org
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