[gmx-users] question regarding high temperature simulation in Gromacs
Quyen V. Vu
vuqv.phys at gmail.com
Wed Jul 4 22:08:24 CEST 2018
Dear Prof. David,
Could you kindly describe in more detail for give me references which
problems will happen?
On Wed, Jul 4, 2018, 15:13 David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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.
> > Regards
> > 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.
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