Regarding gmx distance

[ikuma]

GROMACS version:2020.2
GROMACS modification: Yes
Dear users,

I’d like to calculate distance between a center of mass on molecule and specific 3d coordinate in my simulation box(e.g. center of PBC).
Can I calculate it with gmx distance? As far as I understand, gmx distance calculate distance between a pair of atom or group, not distance between specific coordinate and a group.

Best,
Kimu

[alevilla]

Hi,
here you can find the difference between gromacs tools that calculate distance. I hope it help to find the best tool

What is the difference between gmx distance, gmx mindist and gmx pairdist?

Hi, I am trying to compute distance between four residues of a protein involved in active site. I am getting confused in mindist, pairdist and gmx distance. What are the limits and differences in three? Which analysis can be helpful in plotting distance between A-B, B-C, C-D and D-A residues over time, where ABCD are 4 residues forming bottleneck for ligand entry.

\Alessandra

[ikuma]

Hi Alessandra,
thank you for your reply.
I’ll check it.

Best Regards,
Kimu