[gmx-users] (no subject)

Dan Gil dgilgmx at gmail.com
Tue Aug 16 23:14:13 CEST 2016


On gromacs 4.6, the use of g_dist explicitly states "the molecule in the
input trajectory should be whole (e.g. by preprocessing with trjconv
<http://manual.gromacs.org/archive/4.6.5/online/trjconv.html> -pbc) or a
matching topology should be provided."
If you want to calculate the distance between the center of mass (COM) of
two groups of residues, you need to have the mass of the residues. I
imagine that you are having issues because your trajectory isn't whole. Do
you at least have the masses of the groups you are interested in? Writing
your own code to calculate the distance might be an easy solution.

On Tue, Aug 16, 2016 at 7:08 AM, Shubham Sehrawet <
shubham.cristiano3 at gmail.com> wrote:

> Dear users
> I have been trying to find distance between the centroids of two groups of
> residues. I have a trajectory file that was created on some other
> simulating platform. Therefore, I do not have the run input file (tpr) and
> I am not able to perform the analysis.
> Can you please suggest me some way to tackle the problem.
> Thank you
> Shubham
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