9 Questions 29 Answers 0 Followers
Questions related from Dr. Rohan Meshram
I have performed MD simulations and obtained binding free energy using MMGBSA. Say it was -30 Kcal/mol. Later on, I separately computed entropy (T-Delta-S) for the same system. The said entropy...
27 March 2025 2,036 0 View
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 5,628 3 View
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 6,025 8 View
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 4,289 5 View
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 4,306 9 View
This question is quite relevant for people working on AutoDock using PyRx. It generates dlg files and provides binding free energy values. But it seems to be a dead end if one wish to generate...
02 June 2014 7,277 8 View
My work being centered around structure based drug design,I have always wonder what might be the exact reason behind the unavailability of structural model of human COX 2 (gene PTGS2). By that I...
27 May 2014 2,585 4 View
My initial compound library had 348,276 compounds. After applying various filters like functional group filters, Physio-chemical filters, removing duplicate compounds, removing Pan Assays...
19 February 2014 8,340 6 View
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 5,176 2 View