[gmx-users] Group vs Verlet pair-lists

[leila salimi]

Thanks Justin.



On Wed, Jul 16, 2014 at 8:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/16/14, 2:21 PM, leila salimi wrote:
>
>> Dear GROMACS Users,
>>
>> I have a question regarding the Neighbor searching, I used group scheme
>> when I used 4.5 and now I found that there is verlet in version 4.6. When
>> I
>> compare the trajectories, For verlet simulation I found that the atoms of
>> water molecules are separated and it caused the long bond in vmd. I mean
>> that one hydrogen is located on the right side of the cell and the oxygen
>> and another hydrgon are on the left side that the first hydrogen can come
>> with periodic image, but these long bond (artifact bonds) are not
>> convenient and it is difficult for visualization.
>>
>> I did not have this problem with previous method (group). Could you
>> explain
>> me what it is happened in  Cut-off schemes = verlet?
>> And is it possible to have the trajectory with the right bonds (not broken
>> bond)?
>>
>>
> This is a normal consequence of PBC and is not related to the cutoff
> scheme. Fix with trjconv -pbc mol or use VMD tools (
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23787.html).
>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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