[gmx-users] Increase temperature to 550K => simulation techniques ?

[Chih-Ying Lin]

Hi
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 ?


Thank you
Lin






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.

-Justin

Chih-Ying Lin wrote:
>
> Hi
> the water model is TIP3P.
>
> Thanks
> Lin
>
>
>
> 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
>