[gmx-users] Problem in mdrun

[tasneem kausar]

Dear All

I am performing MD simulation of protein and drug in Gromacs_4.5.4 using
amber99SB force field with tip3p water model. I have successfully generated
the tpr file for full MD simulation with two drugs. I have some other drugs
to simulate with the same protein. Everything goes smoothly till the energy
minimization giving a negative potential energy value. When I am try to run
position restrain, mdrun is not generating any output. There is no error or
warning massage. I have enough disk space of around 125 GB. I have tried
mdrun at another PC and also at Gromacs_4.6.3.

Here is my mdp file for position restrain.
;
;    User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
constraintalgorithm =  LINCS
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  50000    ; total 100 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  0.9
coulombtype         =  PME
rcoulomb            =  0.9
rvdw                =  1.4
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 in two groups
Tcoupl              =  berendsen
tc-grps            =  Protein    Non-protein
tau_t               =  0.1    0.1
ref_t               =  300    300
; Energy monitoring
energygrps        =  Protein    Non-protein
; Pressure coupling is not on
Pcoupl              =  no
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

Kindly tell me where I am missing.

Thanks in advance.

With Regards
Tasneem Kausar