[gmx-users] Blowing up
jalemkul at vt.edu
Mon Aug 10 19:46:05 CEST 2015
On 8/10/15 1:42 PM, faride badalkhani wrote:
> Dear Victor,
> Thanks a lot for your answer. Could you introduce me a guidance for
> defining proper charge groups?
The error message provides guidelines on what to do. With the Verlet scheme,
charge groups are ignored. Without a better description of what you're doing,
what your .mdp settings are, etc. there's little point in guessing here.
> Truly yours,
> On Mon, Aug 10, 2015 at 5:44 PM, Victor Rosas Garcia <rosas.victor at gmail.com
>> it could be, but it might just be easier to try redefining smaller charge
>> groups and run the dynamics again.
>> Hope this helps
>> 2015-08-09 2:16 GMT-05:00 faride badalkhani <farideh.khamseh at gmail.com>:
>>> Dear all,
>>> I am truing to do an MD simulation on dendrimeric structures. I can
>>> all steps successfully, but I get a NOTE in all steps after Adding Ions
>>> NOTE 2 [file topol.top]:
>>> The largest charge group contains 20 atoms.
>>> Since atoms only see each other when the centers of geometry of the
>>> groups they belong to are within the cut-off distance, too large charge
>>> groups can lead to serious cut-off artifacts.
>>> For efficiency and accuracy, charge group should consist of a few
>>> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>> Finally at the production MD step I get a "X particles communicated to
>>> node Y are more than a cell length out of the domain decomposition cell
>>> their charge group".
>>> Do you think is it because of the mentioned note?
>>> Truly yours,
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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 629
University of Maryland, Baltimore
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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