GROMACS version:
GROMACS modification: Yes/No
Dear users,
I created an index.ndx file in which I defined the group which encompass only my protein (eventually with ions or cofactors) and the ligand of interest. Then, in the md.mdp file I set “non-Water” and “Water” as tc-grps groups and “non-Water” as the xtc-grps. The first question is: does it make sense?
In addition, now I have one more problem: when I try to bring the protein in the center of the box (by using gmx trjconv) I have the following error
Fatal error:
Index[6942] 6943 is larger than the number of atoms in the
trajectory file (6942). There is a mismatch in the contents
of your -f, -s and/or -n files.
I tried with convert-tpr but it does not fix the problem.
Any hints?
Thanks in advance