Wan Chap Wong

4 Questions 6 Answers 0 Followers

Questions related from Wan Chap Wong

What is the fastest way to extract a single time frame from a large trr file in Gromacs?

I have a very large trr file generate in Gromacs. I need to extract an single time frame in specific time. I know I can do the following: trjconv -f md.trr -s md.tpr -o frame.pdb -dump time But it...

01 January 2015 9,049 4 View

Does gromacs have any tool to export the z matrix of protein?

I need to extract the z matrix or internal coordinate of protein in the gro or trr file. Does gromacs have such build in tool? If no, is there any external tool can do so?

01 January 2015 6,982 1 View

How to convert .pdb in PYMOL to .gro in GROMACS?

Whenever I need to convert a pdb file from PYMOL to GROMACS, the ordering and name of atom inside the residue is different from those inside the default force-field. So whenever I convert a pdb to...

12 December 2014 5,923 11 View

How do you get the potential of protein (excluding solvent) in Gromacs

In gromacs, we can get the potential of the system (including solvent) in .edr file. However, in my case, I need to get the potential of the protein only (excluding solvent). How do I calculate...

08 August 2013 3,695 6 View