Lakshmanji Verma

6 Questions 7 Answers 0 Followers

Questions related from Lakshmanji Verma

Why partial charge on chlorine atom from GAFF is +ve?

I am looking for an Amber based force field for chloroform as solvent to use with Gromacs. I adopted GAFF ff from http://virtualchemistry.org. The partial charge on chlorine and carbon which are...

08 August 2019 8,449 4 View

Which thermostat and pressure couple are preferred for MD and why?

I have simulated my system with two thermostat, Noose-hoover and V-rescale, with same pressure couple. I got slightly different results for the two different thermostat. What could be the possible...

06 June 2018 4,148 2 View

Gromacs PBC: What the difference when I put periodic-molecules "yes" or "no" with pbc in all xyz direction?

I checked it in the manual which says if periodic-molecules is set to no, "molecules are finite, fast molecular PBC can be used" and if it is set to yes " for systems with molecules that couple...

04 April 2018 4,569 0 View

Is there any way we can corelate CSP data with MD simulations?

I would like to if there is any way to correlate experimental CSP data with that of MD simulation. If possible, please suggest me some papers.

10 October 2017 399 2 View

DNA-Protein complex simulation with GROMACS using Charmm36 Force field.

I have simulated a DNA-Protein Complex structure with 150mM NACL salt concentration for 100 nanoseconds. The simulation is completed with not much problem, but while visual analysis in VMD of the...

05 May 2017 8,213 10 View

How to incorporate NMR Chemical Shift data as restraint in MD for protein-ligand complex?

I am more interested in learning the process of doing it and not just outcome.

02 February 2017 1,884 2 View