GROMACS version: 2020.4
GROMACS modification: No
does anyone know whether there’s a way to use dynamic selections with tools such as trjconv?
I’d like to use some analysis tools such as gmx msd to understand the behavior of my solvent, but only in the vicinity of my polymer.
One approach I tried was to use gmx select to get the indices that were in the vacinity of the polymer at each timestep, i.e. using gmx select and going:
resname SOL and within 0.5 of group "polymer"
… which gives me the atom indices which satisfy this criteria as a function of timestep in an index file.
Passing this index file to analysis tools such as trjconv to output those atoms in the viciniity of the polymer at each timestep doesn’t work - the closest I get is a trajectory which includes all atoms that will at some point be in the vacinity, rather than only those at each timestep.
Any suggestions would be greatly appreciated.