Sanjoy Paul

5 Questions 16 Answers 0 Followers

Questions related from Sanjoy Paul

What does the raw variance-covariance ascii data file contain in GROMACS ?

I performed Principal Component Analysis (PCA) using GROMACS 5.1.3 with the following command gmx covar -f filename.xtc -s su2-now.gro -n protein-H.ndx -o eigval.xvg -v eigenvec.trr -ascii...

16 August 2016 8,085 8 View

Why is the combination of nose-hoover thermostat and MTTK barostat not working during NPT equilibriation of a protein in GROMACS ?

I tried to perform NPT equilibriation on a protein with nose-hoover thermostat and MTTK barostat with the following .mdp file ; VARIOUS PREPROCESSING OPTIONStitle = NPT simulation (constant...

12 July 2016 1,814 8 View

How to modulate velocity rescaling in gromacs during heating of a protein ?

I was trying to heat my protein system from 0 K to 300 K using the following temperature coupling tcoupl = v-rescale ; modified Berendsen thermostattc-grps = system ; one coupling grouptau_t = 0.1...

01 June 2016 8,045 16 View

How can I run a MD simulation in gromacs keeping protein heavy atom fixed ?

Hi, I was trying to run heating of a protein keeping all protein heavy atom fixed in its' crystal structure position using GROMACS.I found that gmx genrestr helps to make a .itp file which...

02 May 2016 6,559 4 View

Why volume of a water-box cube containing a protein (128 residue metalloprotein) is not getting converged in NPT equilibriation MD simulation ??

When we perform MD simulation of a protein in a solvent box at constant temperature presssure condition then we generaly see that initially volume gets decreased and then fluctuate around a...

27 September 2015 5,725 6 View