[gmx-users] Listing residues in gromacs

Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delhi

[gmx-users] Listing residues in gromacs

Hi, Is there any option in gromacs to list residues/atoms around a reference group? I have checked trjorder , but it only gives number of molecules. Thanks & Regards, -- *Subhomoi Borkotoky, Ph. D.* Kusuma School of Biological Sciences, Indian Institute of Technology Delh

Re: [gmx-users] Listing residues in gromacs

Hi Subhomoi, Yes, gmx select can do that (see http://manual.gromacs.org/documentation/2020/onlinehelp/gmx-select.html) For what you want to do, it's beneficial to have a look at the selection syntax here http://man

Re: [gmx-users] Listing residues in gromacs

Hi Christian, Thank you for your reply. The command worked well. I got the indices of the residues. I want to calculate the occupancies of the residues near my reference ion within say 0.5 nm. It will help me a lot if you could suggest something for it. I have tried gmx distance and gmx mindist wi