priya thiyagarajan wrote:
hello sir,
thanks for your kind reply..
in another folder i resubmitted my mdrun from starting time..
i reduced my time step..
i kept my time step = 0.001
this is my md.mdp file
title = Gromacs43a1 lipopeptide MD
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 5000000 ; 1 * 5000000 = 5000 ps, 5 ns
dt = 0.001 ; 1 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = *V-rescale* ; modified Berendsen thermostat
tc-grps = DRG SOL ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
i resubmitted my mdrun and my run completed i analysed my output file..
now it completed at 1.286ns out of 5ns..
in log file it didnt give any information about this error..
in error file its showing segmentation fault..
how to solve this prolem..
Mark already provided this link, but I'll post it again anyway:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
On that page you will find not only several possibilities as to the source of
the problem, but also the means to diagnose what might be going wrong. Please
pay careful attention to this page, as it summarizes this information very well.
is it only because of some problem in my system??
Yes, quite likely. The questions that come to mind for me - what is DRG? What
is its topology? Did you do proper energy minimization and equilibration?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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