[gmx-users] problem with exchange probabilities in remd
David van der Spoel
spoel at xray.bmc.uu.se
Sun Feb 24 09:58:49 CET 2008
OZGE ENGIN wrote:
> Hi all,
> I am performing a remd simulation of a peptide+water system. I have tried different temperature distributions. I am using an NVT ensemble. My temperature coupling constant is 0.1 ps.
I was going to suggest out webserver http://folding.bmc.uu.se/remd/index.php
when I realized you're doing NVT simulations (which we don't support
yet). Why are you using NVT? It will mean your high T samples are at
high pressure as well.
> The problem is that upon increasing the temperature difference between the two replicas more than two (290==>294), the exchange probability decreases sharply, app. to 0.03.
> I have changed the exchange frequency in order to get a better exchange probabilities. However, it has not affected the overall exchange probabilities so much.
> Is there anybody who has encountered such a situation?
> Thanks in advance
> Ozge Engin
> Computational Science & Engineering
> Koc University
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
More information about the gromacs.org_gmx-users