7 Questions 6 Answers 0 Followers
Questions related from Ajit Kumar Singh
I have a membrane model files from a published work. I want to use that model for my research. Can anyone help me with how do I proceed with it. I have the PDB, PSF and STR files of the membrane....
29 June 2024 6,490 1 View
I have 4 replicas in my REMD simulation of a small peptide. The replicas temperature is 298, 302, 306 and 310. As I am doing REMD for the first time I have no idea on how to process these 4...
22 November 2023 4,084 0 View
I am familiar with Conventional MD Simulations using GROMACS. And I want to learn other advance MD methods. If I can get some help with Replica Exchange Molecular Dynamics (REMD/REST), How to run...
09 November 2023 5,230 0 View
I have two structures Fe2O3 and Fe3O4 nanoparticles with a diameter of 5 nm. I want to perform MD simulations on the two nanoparticles, but non of the force fields have parameters for these...
02 June 2023 7,956 1 View
I have a pdb file and want to add numbering at 24 column in every line, how to do this using command or a tool?
15 September 2022 9,926 0 View
Tried "gmx covar" but didn't got the expected results. Please help.
20 January 2022 8,093 6 View
The ligand is interacting with chain A of the protein and the RMSD plot shows a sudden rise in first 20 ns and then stabilizes in the later part. Please tell if chains can be separately viewed in...
06 January 2022 3,376 3 View
