[gmx-users] Distance between COM of two groups

[Justin Lemkul]

On 6/18/16 9:40 AM, Sajjad Kavyani wrote:
> Dear experts,
>
> I am puling group2 toward group1 and I want to calculate the distance
> between COM of two groups versus time.
> For the g_dist it was a straightforward process with the selection menu.
> But for the "gmx distance" I used:
>
> gmx distance  -f test.xtc -s test.tpr -oav -oxyz -n index.ndx
> -select 'com of group "group1" plus com of group "group2"'
>
> But both outputs distances are a growing value over time (!!)
> (actually the average value is the same with sqrt(x^2+y^2+z^2)) where
> the distance meant to be decrease over time!
>
> Could you please help me with the commands?
>

That's the correct command.  Is there some reason why you think the result is 
wrong?  Are your group definitions correct for the analysis you're trying to 
perform?

-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

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