[gmx-users] Suggested settings for using Amber force field in Gromacs
jalemkul at vt.edu
Thu May 5 15:24:55 CEST 2016
On 5/5/16 9:20 AM, Casalini Tommaso wrote:
> Thanks a lot for your quick answer.
> I am trying to reproduce with Gromacs some results that I obtained with Amber software.
Is there some discrepancy between the two that you're trying to resolve?
> I put the same thermostat (Langevin) and barostat (Berendsen with isotropic scaling) with same time constant, the same dt, the same cutoff, and so on.
> I was wondering if there are some other settings concerning thermostat, barostat and long range interactions which should be changed in order to be consistent with Amber default.
Each program should have more or less comparable settings, but there are always
algorithmic differences between software that complicate such comparisons (see
the extensive discussions on this topic in recent weeks). But by using the same
settings, you should be able to reproduce results on average. There are no
special considerations as far as GROMACS is concerned. The application of a
force field is the application of a force field; no special tricks required.
> Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] per conto di Dries Van Rompaey [dries.vanrompaey at gmail.com]
> Inviato: giovedì 5 maggio 2016 15.05
> A: gmx-users at gromacs.org
> Oggetto: Re: [gmx-users] Suggested settings for using Amber force field in Gromacs
> Your first stop should be the article describing the parametrisation of the force field. It might also be useful to look for articles that are doing something similar to what you want to do.
>> On 05 May 2016, at 14:49, Casalini Tommaso <tommaso.casalini at chem.ethz.ch> wrote:
>> Dear Gromacs users and developers,
>> I would like to use Amber force field in Gromacs.
>> I have no problem for topology conversion and so on, but I would like to ask which are the best settings which should be used for the simulation.
>> Right now I am using Berendsen barostat (which is implemented in Amber), PME for electrostatic interactions and Langevin thermostat. I have also put DispEner = no.
>> I would like to ask if you can provide some suggestions for the best settings that, in your experience, should be used for simulations using Amber force field.
>> I thank you in advance for your help and collaboration.
>> Tommaso Casalini
>> Posdoctoral fellow, ETH Zurich
>> 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.
> 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.
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
More information about the gromacs.org_gmx-users