[gmx-users] Protein-Protein distance

[Justin Lemkul]

On 1/5/16 1:18 AM, Life Sciences Inc wrote:
> Dear Gromacs Users
>
> Kindly let me know how to calculate the protein protein distance as a
> function of time with gromacs. I want to calculate the distance based on
> the center of mass of the selection which is CA atoms. I have 4 proteins in
> the system and want to calculate the distances as distance between Protein
> 1 and Protein 2, then Protein 1 and Protein 3 , then Protein 1 and Protein
> 4.
>
>
> I used gmx mindist command but it cannot be used to calculate distance with
> center of mass, I tried gmx distance also, but do not know how to use it
> for my above mentioned purpose.
>

gmx distance is the correct command, but you haven't told us what you've tried 
and why it didn't work (or why you think it didn't work), so it's not productive 
for us to simply guess.

-Justin

-- 
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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

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