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

Justin Lemkul jalemkul at vt.edu
Fri Nov 8 14:46:24 CET 2013



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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