Hello,
I am trying to perform a simulation run of 10ns for my system
[protein+waterbox].The system works fine if i use timestep[dt=0.002
fs]. To balance the run time and time-consumption, when we try a
.mdp file with slight increase of timestep i.e., to 0.003 fs; grompp
works fine and generates input tpr, but when going further with mdrun,
the program crashes, giving error:
"Segmentation Fault"
So i have to increase the number of steps[nsteps] to achieve required run
time.But this'll be time consuming.I am unable to figure out any
alternative.
I am using Gromacs 3.3 on IBM Power5 machine with SLES9.
Please suggest me the required to be done.Thanks in advance.
The .mdp file i've used:
integrator = md
;Total simulation time: 5000 ps
:time step in femtoseconds
dt = 0.002
;number of steps
nsteps = 2500000
nstxout = 100
nstvout = 100
nstlog = 10
nstenergy = 10
nstxtcout = 10
;xtc_grps = prot
;group(s) to write to energy file
energygrps = protein non-protein
Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist = 10
cut-off distance for the short-range neighbor list
rlist = 0.8
;treatment of electrostatic interactions
coulombtype = PME
rcoulomb = 0.9
*********$$$*********
Ramya Cherukupalli,
Final year,
M.S Bioinformatics,
IIIT - H.
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