Dear All,
I am trying to do position restrained dynamics of a protein with
co-factor in Gromacs Version 4. But after running for a while (1390
steps), the run is simply stopping. I am not getting any message on
log file or terminal. Please help to identify the problem.
This is my pr.mdp file parameters:
; User 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 = 15000 ; total 30 ps.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
; temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling is on
Pcoupl = Parrinello-Rahman
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
Thank You,
Regards,
Sukesh.
--
Sukesh Chandra Gain
TCS Innovation Labs
Tata Consultancy Services Ltd.
'Deccan Park', Madhapur
Hyderabad 500081
Phone: +91 40 6667 3572
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
