[gmx-users] Clarification on gmx mindist

Hi. This is in context of protein-protein simulation.One of my protein is a 167 residue chain(receptor), the other protein is a 41 residue peptide (ligand). I am using mindist with the -or option to see how my ligand comes close to my receptor protein.

[gmx-users] Reference atoms for gmx mdmat and gmx rmsf

Hi gmx-users, There are a few things I wanted to know: 1. For RMSF calculations, which atoms are used when I am calculating RMSF for a group specified in the index? 2. For gmx mdmat , for 2 protein chains taken together i.e using the Protein group , "sma

Re: [gmx-users] Reference atoms for gmx mdmat and gmx rmsf

or groups you specify in your selection > string. If you say, e.g. "protein and name CA" you will get all C alphas in > the protein(s) in your system. See here > http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html > > On Thu, May 17, 2018 at