[gmx-users] process getting killed

[P.R.Anand Narayanan]

Dear gromacs users,
I ran a md simulation for 2ns with the mdp file as shown:
er spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000    ; total 10 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; 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
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529

it was successful, but then while using the trajectory convert; ie, to a xtc file and also while using g_rms and g_gyrate command, it got killed. So i modified the mdp file and re-ran the md simulation for 2ns; the mdp file is:
er spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  1000000    ; total 2 ns.
nstcomm             =  1
nstxout             =  2500
nstvout             =  2500
nstfout             =  100
nstlog              =  1000
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; 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
igen_seed            =  173529

But still it was getting killed; ie, the xtc, and xvg file conversions.
Please help as to how i can overcome this problem.
thank you



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