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

[Mark Abraham]

Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).

Mark


On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Thank you, Mark. I think that running it on CPUs is a safer choice at
> present.
>
>
> On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > 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.
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html
> > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > --
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>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
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