Kalyanashis Jana

5 Questions 8 Answers 0 Followers

Questions related from Kalyanashis Jana

How can I easily get Tm (thermal mid point, i.e., thermal stability) of a protein using only PDB ID?

I am interested to collect thermal stability of different proteins, i.e., their Tm values. Is there any easiest way to find the Tm using only RCSB PDB ID? Suppose I would like to get Tm value of...

02 February 2019 5,811 4 View

How to interpret potential mean force profile obtained using g_wham?

Dear all, I have performed steered molecular dynamics simulation for protein drug complexes using Gromacs simulation package. To get potential mean force profile, I have used "g_wham -it...

11 November 2017 1,315 0 View

How to do Replica Exchange Molecular Dynamics (REMD) analysis?

I have performed an REMD simulation for protein drug system (8350 + 32500 sol) using gromacs-4.4.5 package. But I could not understand how to do analysis of REMD. I have used 10 set of replicas...

11 November 2016 9,363 5 View

How large solvation energy value would be reasonable with g_mmpbsa tools?

Dear all,I have been trying to calculate MMPBSA free energy. I have followed the procedure describe in http://rashmikumari.github.io/g_mmpbsa/. However, I am confused with too large value of...

01 January 1970 9,348 0 View

How to do MD simulation for two or more peptide chain using Gromacs Simulation package?

Dear all,I would like to run an MD simulation for two or more peptide chain. I gotthe following error in the steepest descent energy minimization step. Couldyou please suggest me, how can I do the...

01 January 1970 4,858 6 View