Ajit Kumar Singh

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Questions related from Ajit Kumar Singh

How to simulate a preprepared membrane model?

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 6,421 1 View

How to process the REMD trajectories obtained from REMD simulation?

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 4,036 0 View

How to run replica exchange molecular simulation in GPU based servers?

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 5,189 0 View

How to generate topology parameter files for Fe2O3/Fe3O4 (Hematite/magnetite) nanoparticles for MD Simulation studies?

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 7,921 1 View

How can I do Cross-correlation matrix and PCA analysis of a Protein in GROMACS after MD simulation?

Tried "gmx covar" but didn't got the expected results. Please help.

20 January 2022 8,038 6 View