Pavel I. Semenyuk

4 Questions 6 Answers 0 Followers

Questions related from Pavel I. Semenyuk

How to read gmx hbond 2018 output?

Hi, please help me to read output of gromacs gmx hbond. There are 3 columns: time, h-bonds, and all pairs with no filter on the angle. @ s0 legend "Hydrogen bonds" @ s1 legend "Pairs within 0.35...

02 December 2022 8,140 3 View

What is the best way for mobility estimation in GROMACS?

I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...

20 January 2021 815 3 View

PE-DB Protein Ensemble Database - does it works?

Does anybody know? The site http://pedb.vib.be/ seems to do not work. Maybe, it is located now in different site?

23 October 2020 6,513 2 View

How to view actual parameters for all dihedrals in topology in gromacs after pdb2gmx?

I have added new residue in forcefield as a *.rtp file and then use pdb2gmx to get topology from *.pdb, but something is wrong because simulation causes LINCS WARNINGs, bond rotations etc after 20...

16 January 2017 8,778 3 View