GROMACS version: 2018.8
Hello,
I am using the COM pulling options in my .mdp file. The distance of the COM of a group is outputted by default. But at the same time, I also want to get the velocity of the pulling groups. I could use the results of the distance of the COM to calculate the velocity by \Delta D/ \Delta t, but the problem is that the fluctuation is extremely high and the data becomes useless. Although some data smooth methods can be used to reduce the fluctuation, the result is still not very very good and I do not know whether the calculated velocity is still reliable. Does Gromacs support output the velocity of the COM of a pulling group directly? Or could you please suggest any workaround?
Any help would be much appreciated!
Gromacs writes the velocity of individual atoms, what about summing the velocity of the targeted group of atoms?
Hello, thank you very much for the advice! Yes, I think it should work although it is not directly from the output. Then I guess I need to change the output format of the trajectory file to .trr file. Could you please also give me some advice on how to do the post-process? Should I use VMD for this? Normally I only use VMD to visualize the trajectory. Thanks in advance!
There might be a better way. I would convert trr to gro file, which is human-readable format. Then parse velocity from gro file, and analyze. I am not sure if VMD reads velocity from gro file. MDAnalysis tool can be used too for parsing trr, in that case, you don’t need to convert trr to gro
Thanks very much for the explanation! I will try MDAnalysis.
If I do it as you recommended with gro files, then I guess I need to write my own code to do the job.
And could you please help me with one more question? Do you think is there any way I can extract the accelerations of the atoms?
trr file contains force on atoms, so acceleration extraction should be trivial, given that you know masses
gmx traj -f file.trr -of
Probably, you can use ‘-ov’ option for velocity extraction too
Thank you very much! That is very helpful.
I used gmx traj to calculate the temperature before. I did not notice it can also be used to get the velocity and force. That is cool. I will try that.