[gmx-users] How to measure distance and find salt bridges in GROMACS ?

Hi all, I want to measure distance between two specific residues during molecular dynamics in GROMACS. I am not aware of gmx distance command for distance calculations. Second, I would like to know how to find the salt bridges during the period of molecular simulation. Thank you in advance.

[gmx-users] Percentage of potential SASA of ligands in Gromacs??

Dear All, How to determine the SASA of different ligands in absolute values and percentage of their potential SASA in solution to estimate how buried they are in GROMACS. Thank you in advance. Thanks & Regards, [image: Mailtrack]

[gmx-users] selection of the type of box in molecular dynamics in GROMACS

Hi everyone, I want to know that on what basis we have to select the specific type of a box for a particular protein during molecular dynamics in GROMACS ? Thank you in advance. -- Thanks & Regards, VIKRAM DALAL Research Scholar -- Gromacs Users mailing list * Please se

[gmx-users] CHARMM force file error in gromacs

mol2 files I have attached here my mol2, str, cgenff_charmm2gmx.py and  charmm36-jul2017.ff.tgz. Thank you in advance. -- Thanks & Regards, VIKRAM DALAL Research Scholar Department of Biotechnology Indian Institute of Technology, Roorkee INDIA -- Gromacs Users mailing list *