I would need to check the distance between the two centers of mass of a Protein and of an organic Ligand (the resname and the resnumber of the ligand are both known), inside a system containing the protein, the ligand and solvent, after a MD run. I know that gromacs has the gmx distance tool to get this information from the trajectory file (.trr .xtc) but I haven't been able to get which is the right selection syntax to use to get it, could you please write me down an example?
Thank you very much in advance!
gmx distance -s my_tpr.tpr -f my_xtc.xtc -select '???'
Hi,
You can create index group of protein and organic ligand using make_ndx.
In the selection prompt, use "com of group 1 plus com of group 2". Here group 1 and 2 correspond to group numbers of protein/ligand in your Index file.
Hi,
You can create index group of protein and organic ligand using make_ndx.
In the selection prompt, use "com of group 1 plus com of group 2". Here group 1 and 2 correspond to group numbers of protein/ligand in your Index file.
Sumedha Bhosale Thank you very much, it worked perfectly!
Have a nice day!
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