Edward Valera-Vera

3 Questions 17 Answers 0 Followers

Questions related from Edward Valera-Vera

Why is GROMACS solvate giving me error when trying to use a mixed solvent in -cs?

Currently I'm trying to solvate a protein with a ethanol-water mixture I made and equilibrated. I did as this page says http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents with a box of...

03 March 2018 9,648 5 View

What is the best way of evaluating a docking pose in a GROMACS simulation?

Hello everyone, I'm evaluating docking poses using MD with GROMACS, for that I have two ligands whose poses were correctly predicted by the docking (i.e. RMSD between pose and crystalographic...

11 November 2017 6,041 2 View

How much time takes each step in a GROMACS MD?

Hello everyone, I'm starting to use GROMACS for MD with mixed solvents, so after reading some threads about it, I decided to generate the solvent box using packmol, and the I ran gmx solvate whith...

01 January 1970 7,348 0 View