[gmx-users] Using nose-Hoover thermostat with berendsen barostat
jalemkul at vt.edu
Wed Jul 19 03:12:36 CEST 2017
On 7/18/17 9:23 AM, jay patil wrote:
> The reason for using berendsen is: I thought parrinello is sensitive, it's not wise to use it while equilibrating. So I was trying to use berendsen for equilibration and then production run with parrinello.
> One more thought, my system is not well equilibrated, I know because it got disturbed when I pulled one water molecule from solvent region into the bilayer. Which disrupted the Bilayer a little bit. Then my system should blow up in initial stages only may be because of overlap. Why it is blowing up after few nano seconds of simulation.
Crashes can occur at any time; they're more frequent right at the outset but bad
physics can manifest at any point. If the system ran fine without any biasing
potential, but then you turn on a bias and things become unstable, you should be
troubleshooting whatever restraints you've added, not the barostat. The
pressure instability is a symptom, not a cause.
> Some insights will be helpful.
>> On 18-Jul-2017, at 5:37 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>> The more Berendsen you use, the less physics you get ;-)
>>> On Tue, 18 Jul 2017 13:44 jay patil <jpatil911 at gmail.com> wrote:
>>> Hi Experts,
>>> Can we use nose-Hoover thermostat in combination with berendsen barostat.
>>> When I use grompp command, it gives warning berendsen will not give true
>>> ensemble, and with -maxwarn 1 option I am able to run the simulation. My
>>> doubt is: can we use this combination of thermostat and barostat. Or both
>>> should be berendsen.
>>> Any suggestion will be helpful.
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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