[gmx-users] desired usage of verlet-buffer-tolerance with charmm ff?

[Justin Lemkul]

On 4/7/16 3:55 PM, Christopher Neale wrote:
> Dear users:
>
> Charmm mdp options are listed here: http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM with the following values:
>
> constraints = h-bonds
> cutoff-scheme = Verlet
> vdwtype = cutoff
> vdw-modifier = force-switch
> rlist = 1.2
> rvdw = 1.2
> rvdw-switch = 1.0
> coulombtype = PME
> rcoulomb = 1.2
> DispCorr = no
>
> ;; verlet-buffer-tolerance is not included in that list , so I presume the suggestion is to accept the default value of 0.005 kJ/mol/ps
>
> However, I would have expected:
> rlist = 1.4
> verlet-buffer-tolerance = -1
>
> I realize that issue #1413 ( http://redmine.gromacs.org/issues/1413 ) is still open, but when I use the approach suggested at http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM I get a surprisingly small increase in rlist as nstlist is increased:
>
> Reading file MD.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 10 to 25, rlist from 1.2 to 1.207
>
> I read somewhere that there is buffering in the verlet scheme, but 0.007 nm sure doesn't seem like a lot... I must be missing something?
>

We have thoroughly validated the approach listed above.  Forces and energies 
match between CHARMM and GROMACS and it is the officially endorsed list of 
settings for using CHARMM36 in GROMACS.  You can decrease the tolerance but I 
don't see any reason to.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================