[gmx-users] question regarding high temperature simulation in Gromacs
jalemkul at vt.edu
Wed Jul 4 23:56:27 CEST 2018
On 7/4/18 4:08 PM, Quyen V. Vu wrote:
> Dear Prof. David,
> Could you kindly describe in more detail for give me references which
> problems will happen?
What happens when you boil water? It turns to steam and its volume
expands rapidly. That behavior is not very stable for most barostats.
Beyond that, force field parameters are usually only validated at
ambient temperature and there is no guarantee that their properties will
be valid at extreme temperatures. Using NVT (e.g. constant density)
circumvents these problems to some extent.
> 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.
>>> 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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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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