GROMACS modification: Yes - Plumed
I need to process a replica exchange trajectory - get the protein/ligand centered and remove pbc.
I normally remove water at the last step of processing. Is there a way to remove water on the first trjconv attempt and then continue using trjconv with no water in the subsequent trajectory files?
One of the options for group selection that
trjconv puts up is
Select group for output:, so then generate an index file which contains all the groups you need for the processing you are doing, plus another group that is everything but water.
Okay, thank you. I’ve done this but then run into errors on subsequent steps even after editing the structure file to reflect the new number of atoms. And for many of the trjconv steps I need a tpr file. How do I produce a tpr file without water? Just delete the SOL line in the [molecules] section of the topology before using grompp?
Use the index file you made, process a coordinate file using it, then adjust a topology to suit. Doesn’t actually matter what coordinate file you use, just as long as it has the correct number of each molecule in it.