[gmx-users] question regarding high temperature simulation in Gromacs
Dr. Puspita Halder
puspita at cse.iitkgp.ac.in
Wed Jul 4 13:42:14 CEST 2018
Thanks for your reply. I'd try to run my high temperature simulations with pressure coupling off as per your suggestion.
I was wondering about the simulation parameters (as mentioned in the early post) that I need to change for running high
temperature simulations and should I use simulated annealing protocol for all such simulations?
----- Original Message -----
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: "gmx-users" <gmx-users at gromacs.org>
Sent: Wednesday, July 4, 2018 1:43:22 PM
Subject: Re: [gmx-users] question regarding high temperature simulation in Gromacs
Den 2018-07-04 kl. 09:11, skrev Dr. Puspita Halder:
> Hi All,
> I have been recently using Gromacs 5.1.4 version for simulating my protein systems (mainly prion protein and some of its mutants). I'd like to perform high temperature (400K or 500K) simulations with those. Now my question is what should be the values of the simulation parameters e.g., compressibility, tau_p or tau_t at 400K or 500K? I used compressibility = 4.5e-5 and tau_p = 2.0 and tau_t = 0.1 for pressure and temperature coupling for simulations at 300K. What other parameters should I change for high temperature simulations? Should I always use simulated annealing protocol for simulations at higher temperature or I can directly heat the system to such higher temperatures? Any comments or suggestions in this regard will be highly appreciated.
> Thanks for your help in advance.
> Puspita Halder
Simulating above the boiling temperature of water may be problematic
with pressure coupling. Better turn it off.
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users