[gmx-users] Barostat Selection
jalemkul at vt.edu
Wed Sep 30 03:10:28 CEST 2015
On 9/29/15 9:06 PM, Parker de Waal wrote:
> Thank you for the prompt response Justin.
> I was unaware that the relaxation time had no effect on simulation performance. Would you expect a difference between tau_p = 1.0 and 5.0 for production runs using Parrinello-Rahman?
Expect a difference with respect to what? All you're doing is changing how
quickly the barostat responds to changes in pressure. Either value is probably
fine for most purposes.
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
> Sent: Tuesday, September 29, 2015 9:00 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Barostat Selection
> On 9/29/15 8:57 PM, Parker de Waal wrote:
>> Hi everyone,
>> I recently got into an interesting discussion regarding barostat selection for NPT equilibration and later NPT production runs and was wondering what the community thought on this issue.
>> Specifically, for the initial NPT equilibrium, would it be acceptable
>> to use the berendsen barostat (tau_p = 1.0 ) and then later switch to
>> the Parrinello-Rahman barostat (tau_p = 5) for production, or would it
>> be best to stick with berendsen (keep tau_p = 1.0 or increase to 5.0
>> to increase ns/day?)
> Barostat relaxation time should have no effect on performance. The Berendsen weak coupling algorithms do not produce correct distributions and they should not be used for production simulations. The algorithm is good for equilibration, but shouldn't be used for much else.
> 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
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://secure-web.cisco.com/1ojLfbMlRYuefZ_1olbKjXPZp-h4B9atVOLOfNXQ7pczhcSv3VkmPlIgK3dmbOVGiGwMhCTCoZzv_jrbSSl3rJC35FBF34au6FR1lWqNwjUmLk1i-p8rHhXfjXJ8RiLsvoVuIxKtlum35oYjAa7eqmHBr2xfQ0a2cH-V3FI4YDUtttitIzcF1c177lFZnkxF9NEeJigdBkiDZVBjuINkIF7gVdNGETE1r8Eu6XjM24e4/http%3A%2F%2Fmackerell.umaryland.edu%2F%7Ejalemkul
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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
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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