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

rajat desikan rajatdesikan at gmail.com
Thu Nov 7 20:45:26 CET 2013


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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