Dr. Rohan Meshram

5 Questions 20 Answers 0 Followers

Questions related from Dr. Rohan Meshram

What is the exact difference between restart files and restart.old files generated as output during NAMD simulations?

When one Performs MD simulations using NAMD. It generates restart files coordinates (.coor), velocity (.vel) and xsc (.xsc) files. It also generates restart files with extension .old. My question...

19 September 2019 5,534 3 View

What causes skin blackening in visceral leishmaniasis?

I am curious about the reason for blackening of skin during infection of leishmania donovani? Is it due to accumulation of some pigment or something else? If it is due to pigmentation then what...

22 February 2015 5,948 8 View

Regarding amino acid nomenclature, are there are software or codes that revert alternative names of Histidine (HSE/HID) to normal HIS?

I have a molecular dynamics trajectory and I wish to perform further study on the last frame. While generating PSF and during course of MD simulation, NAMD and VMD changes 3 letter code of...

02 November 2014 4,228 5 View

Why are binding free energy values calculated during molecular docking negative?

I just got curious to know what the significance of preferring a pose with more negative value is? What exactly does this negative sign signify?

17 July 2014 4,248 9 View

How to improve the performance by using NAMD for MD on windows OS?

I am using NAMD for MD on windows OS, using +p4 in "+p"On i5 processor uses 100 % CPU but not 100 % memory. How can we make 100% memory utilization?

19 November 2013 5,120 2 View