[gmx-users] Suggested settings for using Amber force field in Gromacs
tommaso.casalini at chem.ethz.ch
Thu May 5 15:21:04 CEST 2016
Thanks a lot for your quick answer.
I am trying to reproduce with Gromacs some results that I obtained with Amber software.
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.
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
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