Vikas Dubey

7 Questions 23 Answers 0 Followers

Questions related from Vikas Dubey

N-linked glycosilation of asparagine in charmm or charmm-gui ?

Hi, I have been try to glycosilate an ASN residue by adding N-acetylglucosamine (GlcNAC). I could find server which does that (http://vienna-ptm.univie.ac.at/) but It gives me the output in...

10 October 2017 7,247 0 View

Best way to model missing residues of crystal structure ?

Hi everyone, I am working with a protein whose first ~20 residues are missing. Experiment evidence suggest that these residues are crucial. So, Intend to model them. However, with so many server...

09 September 2017 426 5 View

How volume remains constant in NVT ?

Hi, I have some background in MD simulations and I am aware of thermostats and barostats. General NVT simulation run parameter file contains only thermostat related information. So, how...

09 September 2016 1,428 4 View

How does one can calculate free energy difference just using simple MD simulations ?

Hi everyone, I have heard about different fancy methods ( e.g. thermodynamic integration, Free energy perturbation, umbrella sampling) but what if I just want to use simple MD to calculate the...

09 September 2016 2,605 3 View

How to solvate membrane-protein system ?

Hi everyone, I am using vmd to create input files for my system. I have protein-membrane system, in which protein is partially solvated in water. I intend to fully solvate the protein and generate...

09 September 2016 2,843 3 View

What's the difference between steepest descent and BFGS minimization algorithm ? and Which one is better ?

Hi everyone, I am interested in performing the free energy calculations for membrane proteins. I am following Justin Lemkul's tutorial for this. In the tutorial, it is mentioned that use of...

04 April 2016 695 5 View

In gromacs, I am constantly getting warning about system is exploding and about 1-4 interaction. Any suggestions how to get rid of it ?

Hi, I am inserting 25mer polyalanine inside the cell membrane vertically. I am interested in calculating free energy of insertion. I am following tutorial of justin lemkul of free energy...

06 June 2015 6,161 7 View