[gmx-users] Re: timestep in CG simulation
agupta at che.ufl.edu
Thu Oct 28 00:28:12 CEST 2004
>> The suggested value of the timestep is 0.05 ps. With this value of
>> timestep the simulation
>> seem to be running fine for some steps (some thousands of steps) and
>> then I get segmentation
>> fault error. Why is this so ? Also if I reduce the timestep to 0.005
>> ps then the simulations run fine.
> Your starting structure is probably allright (since you can run 1000's of
> steps). Were there any error/warning messages before the crash? Have you
> looked at changes in the energies and/or the structure? You could try to
> re-start short before the crash, write out more frames (lower nstxtcout)
> and look at them.
Thanks a ton Anton for the reply .To remind others again, I am running
simulation ( http://md.chem.rug.nl/~marrink/coarsegrain.html) and am
trying to figure out
why a timestep of .05 ps gives me Segmentation Fault after about 48000
a timestep of .005 ps does not.
I tried with different timesteps and found that the system crashes
sooner if I increase my
timestep to 0.055 ps or 0.06 ps
I checked the energies in the system . What I found is the energy
of my system shoots
up in one or two steps. It is the kinetic energy which shoots up first
and then the system
crashes. Any idea why this fast change in energy occurs ( in one or two
steps when the
system has been happily running for some initial steps. )
I checked the velocities in the last saved frame and found that the
velocity of some beads
shoots very high . But I have no idea why the system does so.
I am using a rlist of 1.3 nm and rvdw is 1.2 nm . The system
crashed even when I
update my neighbour list every step. I am using Berendsen temperature
time constant 1 ps.
I am new to gromacs and highly appreciate any help
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