Changdev G. Gadhe

3 Questions 8 Answers 0 Followers

Questions related from Changdev G. Gadhe

MD simulation setup at GPU-Gromacs?

I would like to run Gromacs-2016.4 on GPU, but I couldn't setup the appropriate parameters of mdrun option of Gromacs and resulted in immediate termination of simulation. I given 2 nodes for...

25 June 2018 6,461 7 View

How can I calulate the concentration of a particular solute in MD simulation system?

Hello Experts. I would like to calculate the concentration of a solute (GABA) inside MD simulation cell which is already explicitly solvated with water and counter ions (NaCl). 0.15 M NaCl is...

02 April 2018 6,002 5 View

How to visualize h-bonds between ligand-protein simulation trajectory in VMD?

I performed MD simulation of ligand-protein complex in Gromacs and now I would like to visualize the h-bonds formed between ligand-protein over the course of MD simulation. I tried to set...

30 January 2018 5,385 7 View