[gmx-users] Re: CHARMM .mdp settings for GPU
Rajat Desikan
rajatdesikan at gmail.com
Fri Nov 8 05:32:38 CET 2013
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
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
On Fri, Nov 8, 2013 at 2:20 AM, Gianluca Interlandi [via GROMACS] <
ml-node+s5086n5012329h44 at n6.nabble.com> wrote:
> Hi Mark!
>
> I think that this is the paper that you are referring to:
>
> dx.doi.org/10.1021/ct900549r
>
> Also for your reference, these are the settings that Justin recommended
> using with CHARMM in gromacs:
>
> vdwtype = switch
> rlist = 1.2
> rlistlong = 1.4
> rvdw = 1.2
> rvdw-switch = 1.0
> rcoulomb = 1.2
>
> As you mention the switch function in gromacs is different than in CHARMM
> but it appears that the difference is very small.
>
> Gianluca
>
> On Thu, 7 Nov 2013, Mark Abraham wrote:
>
> > 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 <[hidden email]<http://user/SendEmail.jtp?type=node&node=5012329&i=0>>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 <[hidden email]<http://user/SendEmail.jtp?type=node&node=5012329&i=1>
> >>> 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 <[hidden email]<http://user/SendEmail.jtp?type=node&node=5012329&i=2>
> >>>> 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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>
> -----------------------------------------------------
> Gianluca Interlandi, PhD [hidden email]<http://user/SendEmail.jtp?type=node&node=5012329&i=11>
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------
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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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