[gmx-users] Fwd: Help with Gromacs 5.1 mdp options for CHARMM27 force field

[Szilárd Páll]

On Fri, Dec 11, 2015 at 3:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/11/15 8:49 AM, Rakesh Ramachandran wrote:
>
>> Hi Justin,
>>
>>       Thanks for the reply. Are nstlist and rlist options important for
>> GPU
>> based gromacs and Verlet cutoff ? I am using nstlist value of 40 and rlist
>> of 1.2 are these appropriate for CHARMM36.
>>
>>
> Verlet tunes both of these as needed.  rlist is automatically adjusted to
> never miss interactions.


Small, but important correction: rlist is indeed automatically adjusted,
but it is done such that that the non-bonded contribution to the drift is
lower than verlet-buffer-tolerance (set in the mdp options). Because the
nstlist estimate is a rather conservative one, in practice the non-bonded
drift is approx. an order of magnitude lower than the value set by the
tolerance and at least as long as constraints and PME are involved it far
from being the dominant factor in the energy drift.

Cheers,
--
Szilárd


> The input value is a minimum value; mdrun takes care of the rest.
>
> Moreover why is force-switch a better option than other vdw-modifier
>> options for CHARMM36 ?
>>
>>
> This is the method with which the force field was parametrized.  It is
> absolutely required for membrane systems.  Proteins and nucleic acids can
> be debated, but unless you have a rock-solid, verified, reason to change
> the vdW method, don't.
>
>
> -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
>
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