[gmx-users] Dynamics

RAHUL SURESH drrahulsuresh at gmail.com
Wed Jan 25 18:00:34 CET 2017

from production output of a monomer for 100ns, there s a instability in the
structure from 83ns to 100ns. Also .gro file shows, the protein is out of
the cube.

gmx make_ndx -f md.gro -o index.ndx
trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center -o

I used the above commands to bring the protein to the center of the box.

gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr

And using the above command, extracted a trr file.

Now can I extend this job with this trr file as it is or should i give any
periodic boundary conditions or should take the conformer structure at 80ns
and run for another 50ns?

waiting for your valuable note.
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*

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