Sam Mohel

3 Questions 2 Answers 0 Followers

Questions related from Sam Mohel

Which reference structure better to select in RMSD calculation?

In the step of RMSD calculation using VMD, I have two gro file : one is energy minimized (em.gro) before I stared the remd simulation and another output file.gro which was generated after...

27 February 2022 5,262 4 View

How to find the relation between rmsd and free energy ?

I need to confirm the convergence of REMD simulation within 200 ns per replica so how can I calculate RMSD values with their corresponding free energy in equal-length non-overlapping time windows...

23 February 2022 9,870 1 View

How can i get the relation between RMSD and free-energy?

I need to find the converged conformational sampling within 200 ns per replica between RMSD and free energy in equal non-overlapping time windows like in the following graph?

21 February 2022 4,949 2 View