[gmx-users] rlistlong problem

Mostafa Javaheri 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?
M.Javaheri


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
>> 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
>
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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