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.
-Justin
________________________________________
Da: [email protected]
[[email protected]] per conto di Dries Van
Rompaey [[email protected]]
Inviato: giovedì 5 maggio 2016 15.05
A: [email protected]
Oggetto: Re: [gmx-users] Suggested settings for using Amber force field in
Gromacs
Hi,
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 <[email protected]>
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 [email protected].
--
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 [email protected].
--
==================================================
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
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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 [email protected].
