[gmx-users] Fwd: gmp_distance VS VMD distance analysis VS snapshot

[Antonio Carlesso]

Hi all,

I would like to take the distance over time between two pair of atoms.

I used gmx distance.

to check the value I download the snapshot every 100 ns..

When the distance is within the unit cell everything should be fine.

when the distance increase the value seems not to be correct ( comparison
between snapshot and value returned using gmx distance).

I also double check using VMD and the value seems in agreement with the
snapshot and in disagreement with gmx distance output).



Do you know how to rationalize this different distance values? and for the
same reason can I trust the interaction energy analysis that I made (ele,
vDw and sum of ele + vdW)?



I also find this thread
https://www.researchgate.net/post/How_to_calculate_distance_between_groups_into_the_nearest_image_using_Gromacs
where they suggest to ask this question for clarification



Thank you for your help!