[gmx-users] Increase temperature to 550K => simulation techniques ?
chihying2008 at gmail.com
Wed Nov 11 16:34:29 CET 2009
For running simulaion parameters, people normally not write the
details in their papers.
high-temperature (up to 600 K) simulations of proteins in TIP3P......
any other detailed suggestion about this ?
I agree with Mark's earlier comment; the water model alone is not the most
immediate concern. A colleague of mine is currently doing lots of
high-temperature (up to 600 K) simulations of proteins in TIP3P using the AMBER
force fields. There are plenty of other methodological concerns (pressure
coupling especially); a thorough search of the literature will give you some
insights into what might be wrong. Plenty of groups have successfully been
doing high-temperature MD for a number of years.
Chih-Ying Lin wrote:
> the water model is TIP3P.
> I think the problem is hidden in your water force field model.
> > The simulation system is merely water + one lysozyme.
> > I increase temperate to 550K.
> > Then, the simulation broke.
> > The following message is shown.
> > MX:hpc0011:Remote endpoint is closed, peer=00:60:dd:48:14:5b (hpc0010:0)
> > mpiexec: Warning: task 0 exited with status 1.
> > mpiexec: Warning: tasks 1-2 died with signal 9 (Killed).
> > mpiexec: Warning: task 3 died with signal 11 (Segmentation fault).
> > Anything wrong with the simulation?
> > Thank you
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