[gmx-users] how to distance between COM of two groups of atoms?

[Justin Lemkul]

On 7/1/16 8:56 PM, Ming Tang wrote:
> Thank you Justin,
>
> I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon atoms. I used the following command to calculate the distance between COM of those 2 groups
>
> gmx distance -n index.ndx -select 'com of group "start" plus com of group "end"' -f test.pdb -s topol.tpr -oxyz dist.xvg
>
> and got average distance:4.385, which is not correct as my protein is around 30-nm-long.
>
> is the command I used correct?
>

The value returned is the shortest periodic distance.  Use -nopbc.

-Justin

-- 
==================================================

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

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