[gmx-users] (no subject)

zaved at tezu.ernet.in zaved at tezu.ernet.in
Wed Aug 16 06:41:55 CEST 2017

Hii Everyone

I had performed a 100ns protein-ligand (docked complex) simulation with
gromacs 5.1.4.

The ligand in my case is hydrogen peroxide.

I have removed the PBC effect and centered the protein.

I have used the following commands:

gmx_mpi trjconv -f md.xtc -s md.tpr -pbc nojump -o out.xtc

gmx_mpi trjconv -f out.xtc -s md.tpr -pbc mol -center -o out_1.xtc

I am analyzing the average distance between the protein and the ligand. I
am getting a value of 3.2nm which is too high.

Also in the out_1.xtc, after 10ns itself the ligand is moving all around
the protein.

Unable to understand why its happening!!

Please suggest.

Thank You


Z. Hazarika
Research Scholar
Tezpur University
Tezpur, India

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