Trjconv for removing pbc: -s gro does not yield expected result

User discussions
1

GROMACS version: 2020.3
GROMACS modification: No

Hi,
I have been using gmx trjconv -f abc.xtc -s abc.tpr -pbc mol -ur compact -center to remove periodicity from trajectory of a monomeric protein. It works as expected. However, recently I had to use gro as a reference file (for -s) and I see it does not give me the result which tpr file gives. The tpr file is generated using the same gro file, hence the reference structure is exactly same. The expected result is an intact molecule centered in the box. With gro file, I still get a broken molecule.

I am not sure if the behavior of trjconv has changed with respect to gro and tpr files. If not, is it a bug?

bharat

2

Hi,
the option -pbc mol puts the center of mass of molecules in the box, and requires a run input file (tpr file) to be supplied with -s. One reason is that the tools need to have the molecule definition for this option and a gro file provides mainly information on the position of atoms.
Kind regards
Alessandra

3

Thank you Alessandra, that makes sense. You are right that gro or pdb file does not provide any topological info about the molecule and hence some options may not be compatible with it, seems -pbc mol is one such option.

I had a trajectory with coordinates for protein molecule without hydrogens, and it was not corrected for pbc. I am not sure if there is an easy way to generate a reference tpr file without hydrogens to use for trjconv.

Thank you again for that information.
bharat