Hi Bill & Dac,
Yeah I made mistake in my first mail by saying 'implicit solvent'.
Simulations are running fine by making few changes in parameters. changes are in Bold format.
I don't know how and why there was NaN in previous run But now its alright.
Yes I am checking Temperature and energies at every stage.
Here is mdin:
&cntrl
imin=0, irest=1, ntx=5, iwrap=0, ntxo=2,
nstlim=5000000, dt=0.002,
ntpr=500, ntwx=500, ioutfm=1, ntwr=50000,
ntc=2, ntf=2, cut=8.0,
ntb=1, ntp=0,
ntt=3, tautp=10.0, temp0=320.0
nmropt=1,
/
&wt type='DUMPFREQ', istep1=500 /
&wt type='END' /
DISANG=rest.rst
DUMPAVE=rest.tra
/
Thanks,Hira
On Wednesday, October 23, 2019, 01:01:51 PM GMT+1, David A Case <david.case.rutgers.edu> wrote:
On Mon, Oct 21, 2019, Hira Jabeen wrote:
>I am trying to run MD simulation in implicit solvent.
>In the initial nanoseconds, results are fine but after 90 nanoseconds I
>get an error of NaNs in coordinates and the simulation stops.
Welcome to MD! There are a variety of reasons why a simulation may
experience an instability, even after a long period where things seem
OK.
It's a good idea to visualize your trajectory, paying particular
attention to any non-standard resdidues or ligands you might have.
Also, study the temperature and energy profile that you can get from the
mdout files. Look for any differences between what you see in "good"
segments of the trajectory from "bad" ones.
It's possible that the difficulty goes back to the use of the CHARMM
force field, or to the conversion programs between CHARMM and Amber
formats. That seems somewhat unlikely, since the simulation ran OK for
a long time, and other users have not reported problems.
Aside: your input files are not using implicit solvent (not sure if that
is important or not.)
....dac
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Received on Thu Oct 24 2019 - 04:00:03 PDT
