[gmx-users] MD run failed..

[Kalyanashis Jana]

Dear all,
I am doing an MD simulation of a protein system. Energy minimization step
has been completed smoothly but the position restraint MD run is not
running properly(after 500-900 steps have been stopped automatically). Even
it has not shown any error or anything. I have used a drug molecule in the
cavity of the active site.
When the box size was 10 X 12 X 25, it was run only 100 steps and with 15 X
15 X 28 box size it was run 500-900 steps. I could not understand what is
the problem. Can anyone please help me?

The pr.mdp file is
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.001 ; ps !
nsteps              =  1000000 ; total 1000.0 ps.
nstcomm             =  100
nstxout             =  250 ; ouput coordinates every 0.5 ps
nstvout             =  1000 ; output velocities every 2.0 ps
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  100
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.0
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
; V-rescale temparature coupling is on
Tcoupl                =  V-rescale
tau_t               =  1.0    1.0    -0.1      1.0   1.0
tc_grps             =  SOL    NA     protein   DRG   CL
ref_t               =  300    300    300       300   300
; Pressure coupling is on
pcoupl              =  berendsen ; Use Parrinello-Rahman for research work
pcoupltype          =  isotropic ; Use semiisotropic when working with
membranes
tau_p               =  2.0
compressibility     =  4.5e-5
ref_p               =  1.0
refcoord-scaling    =  all
; Generate velocites is on at 300 K.
gen_vel             = yes
gen_temp            = 300.0
gen_seed            = 173529


Thanks in advance,
Kalyanashis Jana.

-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com