[gmx-users] setting tc-grps and gen-vel

[Justin Lemkul]

On 1/28/17 12:54 PM, qasimpars at gmail.com wrote:
> Dear users,
>
> I am confused on the setting tc-grps, gen-vel, and continuation:
>
> -Do you suggest one or more groups with tc-grps to simulate a protein-ligand complex? That means setting tc-grps=protein water_ions_ligand or tc-grps=system is better? And why?
>

The conventional wisdom is to set the complex and solvent as separate groups. 
The ligand is more intuitively considered "part of the protein" than it is "part 
of the solvent."

> -Do you think that I should set gen-vel=yes and continuation=no in the NVT, NPT and MD step? Is there any (dis)advantage of generating new velocities in all the steps?
>

You should only ever generate velocities once.  What's the point in 
equilibrating if you're just randomizing the system again at each step?  You're 
undoing work that you've already done.  Proper continuation via checkpoint files 
is necessary to have a sane simulation.

-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

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