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

[Rajat Desikan]

Hi Justin,
I take it that both the sets of parameters should produce identical
macroscopic quantities.
For the GPU, is this a decent .mdp?

cutoff-scheme    = Verlet
vdwtype             = switch
rlist                    = 1.2
;rlistlong             = 1.4                     NOT USED IN GPU...IS THIS
OK?
rvdw                   = 1.2
;rvdw-switch        = 1.0                    NOT USED IN GPU...IS THIS OK?
coulombtype       = pme
DispCorr             = EnerPres
rcoulomb            = 1.2


On Fri, Nov 8, 2013 at 7:19 PM, Justin Lemkul [via GROMACS] <
ml-node+s5086n5012351h26 at n6.nabble.com> wrote:

>
>
> On 11/7/13 11:32 PM, Rajat Desikan wrote:
>
> > Dear All,
> > The setting that I mentioned above are from Klauda et al., for a POPE
> > membrane system. They can be found in charmm_npt.mdp in lipidbook (link
> > below)
> > http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html
> >
> > Is there any reason not to use their .mdp parameters for a
> membrane-protein
> > system? Justin's recommendation is highly valued since I am using his
> > forcefield. Justin, your comments please
> >
>
> Careful now, it's not "my forcefield."  I derived only a very small part
> of it :)
>
> > To summarize:
> > Klauda et al., suggest
> > rlist                      = 1.0
> > rlistlong                = 1.4
> > rvdw_switch          = 0.8
> > vdwtype                = Switch
> > coulombtype          = pme
> > DispCorr                = EnerPres     ;only usefull with reaction-field
> > and pme or pppm
> > rcoulomb               = 1.0
> > rcoulomb_switch    = 0.0
> > rvdw                     = 1.2
> >
> > Justin's recommendation (per mail above)
> > vdwtype = switch
> > rlist = 1.2
> > rlistlong = 1.4
> > rvdw = 1.2
> > rvdw-switch = 1.0
> > rcoulomb = 1.2
> >
>
> The differences between these two sets of run parameters are very small,
> dealing
> mostly with Coulomb and neighbor searching cutoffs.  I would suspect that
> any
> difference between simulations run with these two settings would be
> similarly
> small or nonexistent, given that rcoulomb is a bit flexible when using
> PME.  The
> value of rlist is rarely mentioned in papers, so it is good that the
> authors
> have provided the actual input file.  Previous interpretation of CHARMM
> usage
> generally advised setting rcoulomb = 1.2 to remain consistent with the
> original
> switching/shifting functions.  That setting becomes a bit less stringent
> when
> using PME.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
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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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