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

[Justin Lemkul]

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.  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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