Storing Velocities/Forces of Protein Atoms

User discussions
1

GROMACS version: Latest
GROMACS modification: No

I am not very experienced with GROMACS so I apologize if these questions are very simple.

I am simulating a protein in water and trying to store velocities/forces of the protein atoms from the integration. I was hoping to minimize the storage space I need to do this, but unfortunately it appears that the compressed .xtc output has no option to store velocities or forces. So my question is whether there is any way to store velocities and forces in a compressed format similar to a .xtc.

Secondly, assuming that I cannot use a compressed .xtc-like format, I could of course use the usual .trr file. But I only need the velocities/forces from the protein atoms, not the solvent. So I was wondering if I could save storage space by only storing the protein atom velocities/forces. I have not been able to find a simple option to make the .trr file do this in the manner that I usually would with the .xtc. Is there any way to do something like this, only storing the velocities/forces that I need?

Basically I am worried that the combination of an uncompressed file format and unnecessarily storing all of the solvent velocities/forces will lead to unreasonably large file sizes for the sampling intervals I will need (I currently have no issue with positions at these sampling rates, but of course I can use the lower .xtc precision and restrict to protein positions), and I am looking for any possible way around that. I might be on the wrong track entirely of course, so suggestions for any alternative approach are appreciated.

Thank you for your time!

2

There is not.

Not directly, but one possibility is to run your job in short segments, then use gmx trjconv to save only the protein data from the .trr file, then delete the full .trr file and continue your job without appending (gmx mdrun -noappend).

3

Not directly, but one possibility is to run your job in short segments, then use gmx trjconv to save only the protein data from the .trr file, then delete the full .trr file and continue your job without appending ( gmx mdrun -noappend ).

Thank you. I was considering essentially this, but I wanted to confirm that there weren’t any alternatives first. Since GROMACS makes this all so convenient with position data I was slightly surprised at the discrepancy. I really appreciate it!