On 11/5/13 7:19 AM, Kalyanashis wrote:
I have given my .mdp file,
; title = trp_drg
warning = 10
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000 ; total 2000.0 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
; Berendsen temparature coupling is on
Tcoupl = berendsen
tau_t = 1.0 1.0 -0.1 1.0 1.0
tc_grps = SOL NA protein OMP CL
ref_t = 300 300 300 300 300
These settings make no sense. Please read
http://www.gromacs.org/Documentation/Terminology/Thermostats.
; 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
And It is a large protein system containing drug molecule and the atoms of
whole system is near about 16000.
As I did not get any .gro file, thus the MD run was not properly finished.
Please suggest me the probable source this kind error.
The run crashes because your energy minimization effectively failed.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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