[gmx-users] rlistlong problem

[Justin Lemkul]

On 7/20/14, 5:02 AM, Mostafa Javaheri wrote:
> Dear Justin
>
> I set rlist = 1.2 and rlistlong = 1.4 in my md.mdp file and after running
> the simulation both of these parameters switch to this value 1.224 in the
> log file. I’m trying to simulate protein-ligand complex by utilizing CHARMM
> force field and I’m using GROMACS version 5. I would be grateful if you
> could tell me why does it happen? The mdp and log files are attached for
> more details.
>

See detailed discussion here: http://redmine.gromacs.org/issues/1413

The net effect is that rlistlong is not needed, and rlist should be tuned as 
part of the Verlet algorithm, so what you see is correct.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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