[gmx-users] How to use tabulated potentials to do coarse grained simulation?

Catfish SUN catfish.hku at gmail.com
Mon May 26 15:40:50 CEST 2008


Dear all,

I am doing the coarse grained simulation of a water box.
I have generated the tabulated potential between water molecules and
planing to write codes to do coarse grained simulation.
Fortunately, the experts on the gmx-dev maillist told me that I can
use the tabulated function provided by Gromacs.

the following is what I have done step by step:
1. prepare the table_SOL_SOL.xvg(7columns, r,f,f',g,g',h,h')
as I combined all the potentials into one term, the g, g' and h,h' are
all set to zeros.
2. prepare the WAT.gro and WAT.top
3. edit the md.mdp
4. grompp -f md.mdp -c WAT.gro -p WAT.top -o md.tpr
5. mdrun -deffnm md -table table
However, at step 5, I kept on getting the following error messages:
Reading file CGMD.tpr, VERSION 3.3 (single precision)
Segmentation fault

can anyone tell me what is wrong with my input files?
THanks  a lot

the content of WAT.top:
=======================
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              1.0     1.0

[ atomtypes ]
;name  mass      charge  ptype       c6           c12
W1    18.01540    0.0   A            0.0          0.0

[ moleculetype ]
; molname       nrexcl
WAT              1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr   charge
1       W1       1       SOL              WAT        1       0

[ system ]
; Name
WATER CG BOX

[ molecules ]
; Compound        #mols
WAT                1728
================================================

the content ot md.mdp:
================================================
title = waterbox MD simulation
cpp = /usr/bin/cpp ; location of cpp on linux
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps.
nstcomm = 1
nstxout = 1000 ; output coordinates every 2 ps; 500 out put only
nstvout = 0
nstfout = 0
nstlist = 10
ns_type = grid
rlist = 0.8
coulombtype = User
rcoulomb = 0.8
vdwtype = User
rvdw = 0.8

table-extension = 0.8 ;nm
energygrp_table = SOL SOL

fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on
Tcoupl = berendsen
tau_t = 0.1
tcgrps = SOL
ref_t = 300
tcgrps = SOL
ref_t = 300
; Use Energy group monitoring
energygrps = SOL
; Pressure coupling is on
Pcoupl = no
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
================================================



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