[gmx-users] Variation of distance between 2 CA atoms with time

[Justin Lemkul]

On 5/26/15 8:42 AM, Biplab Ghosh wrote:
> Dear Gromacs Users,
>
> I am new to Gromacs and using Gromacs-5.0.4.
>
> I want to calculate the variation of distance between to
> C-alpha atoms in a protein in course of time.
>
> First, I have created a file called: L153_V161.ndx using make_ndx
> and the content of the file is:
>
> [ L153 ]
> 2277
> [ V161 ]
> 2394
>
> Then I was running the following command:
>
> gmx_mpi distance -f protein.xtc -s protein.gro -n L153_V161.ndx -select
> 'com of group "L153" plus com of group "V161"' -oav
>
> I am not getting the distance L153-V163 as a function of time, rather its
> giving me some average distance of L153.
>

I don't understand what you mean.  You can't have a distance of a point.  Your 
syntax correctly specifies how to calculate a distance, so that's what you 
should be getting.  Typically you'd use -oall for a simple distance, but that 
should probably be the same as -oav in the case of a single distance between two 
atoms.

-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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