Narendra Kumar

5 Questions 5 Answers 0 Followers

Questions related from Narendra Kumar

How can I extract only specific snapshots in gromacs trajectory?

I can easily do it by using trjconv -b and -e option if I need to extract only one snapshot. However, if have a list of suppose 5000 snapshots, not in particular order, it gets very...

03 March 2017 4,628 9 View

How do you perform Hamiltonian Replica Exchange in GROMACS?

Hamiltonian Replica Exchange has been implemented in Gromacs. However, a proper procedure to perform H-REMD is not available. Any help on this topic is highly appreciable. Thanks.

04 April 2015 4,267 1 View

When the NVT ensemble is used after equilibration, should the pressure match the specified value?

I used the NVT ensemble and specified 1 bar of pressure. However, after 50ns of simulation it shows the pressure in the range of 100-200 bars. I am now wondering whether this is ok or whether I...

07 July 2013 3,856 14 View

Software to determine the buried or exposed residues of proteins quantitatively

I used VMD to determine the exposed residues of proteins, however, it does not say which residue is of particular amino acid is exposed or buried.

03 March 2013 6,635 3 View

How to replace some amino acids of a protein with the other ones? Which software will be good for that?

I tried in Spdbv and VMD, but could not find.

01 January 2013 1,925 42 View