[gmx-users] Blowing up

[Justin Lemkul]

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.

-Justin

> Truly yours,
> Farideh
>
>
> On Mon, Aug 10, 2015 at 5:44 PM, Victor Rosas Garcia <rosas.victor at gmail.com
>> wrote:
>
>> it could be, but it might just be easier to try redefining smaller charge
>> groups and run the dynamics again.
>>
>> Hope this helps
>>
>> Victor
>>
>> 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
>> perform
>>> all steps successfully, but I get a NOTE in all steps after Adding Ions
>> as
>>> follows:
>>>
>>> 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
>>> charge
>>>    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
>> atoms.
>>>    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
>> PME
>>> node Y are more than a cell length out of the domain decomposition cell
>> of
>>> their charge group".
>>>
>>> Do you think is it because of the mentioned note?
>>>
>>> Truly yours,
>>> Farideh
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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
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================