[gmx-users] Suggested settings for using Amber force field in Gromacs

[Hannes Loeffler]

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
cutoff).


Cheers,
Hannes.