Kithma Sajini

3 Questions 3 Answers 0 Followers

Questions related from Kithma Sajini

How to build a gold nanocluster computationally?

Hello all, I want to computationally design design Au25 nanocluster with attached ligands. I have designed the icosahedron metal core using Open MD. Now I need to attach six -S-Au-S-Au-S-...

24 May 2024 2,532 0 View

Fatal error: Syntax error - File tip4pew.itp, line 5 Last line read: '[ moleculetype ]' Invalid order for directive moleculetype?

Hello all, I want to run a Molecular dynamics simulation by using Gromacs and OPLS AA force field. I'm getting the above error when I tried to run the energy minimization step. Now I don't...

21 June 2023 1,187 3 View

How to calculate the RMSD value of a multiple regions using VMD?

Hello, I have ran MD simulation using NAMD and CHARMM36 forcefield and want to calculate RMSD values of multiple residues.(EX: RESID1 to52,133-193,281 to 296)How can I calculate this using VMD? I...

18 March 2022 5,742 4 View