[gmx-users] Re: CHARMM .mdp settings for GPU

[Mark Abraham]

Hi,

It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the
original paper's coulomb settings can be taken with a grain of salt for use
with PME - others' success in practice should be a guideline here. The good
news is that the default GROMACS PME settings are pretty good for at least
some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU
auto-tuning of parameters in 4.6 is designed to preserve the right sorts of
things.

LJ is harder because it would make good sense to preserve the way CHARMM
did it, but IIRC you can't use something equivalent to the CHARMM LJ shift
with the Verlet kernels, either natively or with a table. We hope to fix
that in 5.0, but code is not written yet. I would probably use vdwtype =
cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2,
but I don't run CHARMM simulations for a living ;-)

Mark


On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan <rajatdesikan at gmail.com>wrote:

> Dear All,
>
> Any suggestions?
>
> Thank you.
>
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