[gmx-users] rlistlong problem
javaheri.gromacs at gmail.com
Mon Jul 21 15:56:14 CEST 2014
Thank you for your explanation, but the question is could I trust the
simulation or not?
On Sun, Jul 20, 2014 at 5:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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 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
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