Ali Jafari

4 Questions 6 Answers 0 Followers

Questions related from Ali Jafari

Performing MD in non-aqueous medium?

Hello everyone, is it possible to prepare a protein for molecular docking using MD simulation in NVT and NPT ensembles and then use the output file in one’s desired solvent and temperature as an...

27 November 2023 3,022 0 View

Why do solvent molecules break apart after executing gmx-solvate command?

Hello everyone I’m trying to run a MD simulation using gromacs software in acetonitrile as solvent but when I execute gmx-solvate command, solvent molecules break apart making the number of atoms...

14 November 2023 298 0 View

What are the steps to run MD simulation using acetonitrile as solvent?

Is it possible to use Acetonitrile as solvent for Molecular Dynamics simulation in GROMACS or DESMOND?

26 July 2023 8,181 5 View

Solvent molecules break apart after executing gmx-solvate command

Hello everyone I’m trying to run a MD simulation in acetonitrile as solvent but when I execute gmx-solvate command, solvent molecules break apart making the number of atoms in .gro and .top files...

01 January 1970 652 5 View