Gmx distance with frame number

User discussions
1

GROMACS version:2020.1
GROMACS modification: No
Dear gmx users,
I am running a CG simulation using reduced units.
How to calculate the distance between two residues with respect to the frame number?
It seems gmx distance only outputs as a function of time.

Thank you.

2

Hi,
you can manually convert the time information in frame number by dividing for the time step.
regards
Alessandra

3

Hi,
Thanks for your response.
I don’t think it is possible because I’m using reduced units. The time values I get from gmx distance has no physical significance with the simulation details.
I wonder there is a method to directly get distance with respect to frame number.
FYI- I used smog2 to generate input files for the coarse grained simulation.

Thanks,
Ashan.

4

Hi,
I know that you use reduced unit. What I mean is that a value for dt is to be set together with nsteps in the mdp file, if you run md or sd (or similar) and the values reported in the x-axis of the distance output file is dt*#nstep (labelled as time)
If you run energy minimization, the x value in the distance output is the frame (even if it is labelled as time).
Best regards
Alessandra