GROMACS version: 2020.4

GROMACS modification: No

Using gmx distance I am able to calculate the average distance and standard deviation for pairs of atoms averaged over the time of the MD simulation. However, I can’t seem to figure out how to do this for angles. All I find are the averages over a set of angles for each time frame. But I would like to find the average for specific angles (a specified triplet or quadruplet of atoms) over the time of the trajectory. Is this possible?

Hi,

An option is to generate the time serie of your angle using gmx angle with the options -ov -all

( “With option `-ov`

, you can plot the average angle of a group of angles as a function of time. With the `-all`

option, the first graph is the average and the rest are the individual angles.” )

then calculate the average using gmx analyze -av (or other tools)

Best regards

Alessandra

Hi Alessandra,

Sure, I already did that as I said (“the averages over a set of angles for each time frame”), but that’s not what want. That gives the average of **a group of angles** at each time step and not the time average of a specific angle. I can, of course, sum over each of the individual angle columns in the output of “gmx angle -ov -all”, but I was looking for an option which would do that for me.

Thanks,

Peter

Hi,

You can run gmx analyze (gmx analyze — GROMACS 2020.4 documentation) on the gmx-angle output (*.xvg file) to get the average.

Alessandra

Hi,

That’s exactly what I was looking for.

Thanks,

Peter