Sandali L.

3 Questions 4 Answers 0 Followers

Questions related from Sandali L.

Which is more suitable for MD simulation of CHARMM-GUI generated files under CHARMM-36 FF? NAMD, AMBER or GROMACS?

I have prepared the simulation files for a protein-membrane system using CHARMM-GUI membrane builder option. The force field used there is CHARMM36 FF. Can you please tell me which MD simulation...

20 June 2022 1,266 2 View

Are Swiss model structures accurate for homology modeling?

In a study, I have to do a comparison between the existing homology models in the literature and the AlphaFold structure by running MD simulations. But only the available homology model is built...

13 June 2022 1,062 2 View

Why .xtc file has not generated in a production md?

I have run the production step for a protein-membrane system using Gromacs. But, the relevant stepX.X_production.xtc has not generated so that I can't proceed to the RMSD analysis. How can I fix...

31 May 2022 7,685 3 View