Hello,
Is there an easy way to generate a new Gromacs trajectory file md_subset.xtc from an existing trajectory file md_allatoms.xtc where I remove everything (including solvent) except a subset of my protein residues?
I believe the Gromacs command "gmx trjconv" has the ability to select subsets of atoms, but I have not been able to figure out how to use it to this end.
Thank you very much for your help!
First select the subset of atoms with make_ndx, and then run trjconv including file.ndx.
gmx make_ndx -f file.gro -o file.ndx
gmx trjconv -s file.tpr -f file.xtc -n file.ndx -o file-out.xtc -center -pbc mol -ur compact
Thank you very much for your help Martiniano. How can I do something similar with a .gro structure file so that, for instance, I can load both in vmd for visualization?
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