[gmx-users] rlistlong problem
jalemkul at vt.edu
Tue Jul 22 01:17:28 CEST 2014
On 7/21/14, 9:56 AM, Mostafa Javaheri wrote:
> Thank you for your explanation, but the question is could I trust the
> simulation or not?
Yes, it's fine. What you observe is expected.
> 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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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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