Subhamoy Mahajan

3 Questions 12 Answers 0 Followers

Questions related from Subhamoy Mahajan

How to correctly generate initial structure of polymers?

I have the topology file for a polymer, i.e. I know all the bonded and non-bonded interaction parameters, but I am unaware of the well-accepted methodology to generate the initial structure. I...

04 November 2019 2,128 5 View

Why do MPI-GPU based mdruns in GROMACS use less memory compared to MPI-OpenMP?

I am benchmarking my coarse-grained MD simulations with 30k beads. I noticed that MPI-GPU based mdruns used less memory and did not change much as I increased the number of nodes. Where as for...

16 July 2018 1,766 3 View

Is the Free Energy Value obtained from a MARTINI Coarse Grained Simulation Scaled by a factor in GROMACS?

I have been trying to finish the polymer tutorial for MARTINI, I was able to reproduce the bonded distribution, and I was also able to get the density, end to end distance and gyration radius...

23 January 2017 5,936 3 View