[gmx-users] tracking position of single particle

[Justin Lemkul]

On 4/20/18 6:35 PM, Jo wrote:
> Hello,
>
> I would like to run a simulation where I need to track the position of a
> single molecule and determine the amount of time it moves a certain
> distance.  Is there a way to do this in gromacs?

Only after the fact, by extracting coordinates from the trajectory with 
gmx traj. There is no way to do this during the run, as it would be 
severely detrimental to performance.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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