[gmx-users] Suggested settings for using Amber force field in Gromacs
tommaso.casalini at chem.ethz.ch
Thu May 5 15:48:42 CEST 2016
Thanks a lot to all, for your insights.
Right now I am running some simulations in order to study the influence of some settings - my ions seem to aggregate more now than in the previous simulations with Amber, but I will wait for longer simulated time.
I am not skilled enough to study the code itself. I also had a careful look at the manuals.
Better, I thought I had a careful look, because I missed the settings that you reported.
Thanks again for you help.
Da: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] per conto di Hannes Loeffler [Hannes.Loeffler at stfc.ac.uk]
Inviato: giovedì 5 maggio 2016 15.40
A: gromacs.org_gmx-users at maillist.sys.kth.se
Cc: gmx-users at gromacs.org
Oggetto: Re: [gmx-users] Suggested settings for using Amber force field in Gromacs
On Thu, 5 May 2016 13:20:59 +0000
"Casalini Tommaso" <tommaso.casalini at chem.ethz.ch> wrote:
> 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.
You will have to carefully study the manuals for both packages (read
the code actually...), check your settings and see how close you can
get. But you will need to accept that differences in implementation
for possible lack thereof may exist. How much your particular system
will depends on such details, I don't know.
BTW, the defaults settings for pmemd/sanders are vdwmeth = 1 (vdW
long-range dispersion correction on) and fswitch = -1 (truncation
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