[gmx-users] Different fluctuation after concatenation

neha bharti nehabharty123 at gmail.com
Wed Nov 12 10:30:08 CET 2014

Hello All

I am trying to perform Molecular dynamics simulation for protein ligand
complex in popc lipid with
charmm36 force field.
Initially my run was of 50ns then I extended by run to 100ns.

The first 50ns run is done in two phase (30ns and 20ns) using cpt file as
there is time limit in supercomputer.
then I concatenate both the .trr files using

trjcat -f md_0_1.trr md_0_2.trr -o md.trr

After that I extend my run to 75ns and concatenate trr file with 50ns file
then again I extend the run to 100ns and perform the same concatenation

the tpr file is extended using
tpbconv -s input_md.tpr -o input_md_extended.tpr -extend 25000

I individually saw the fluctuation of all the trr using VMD. And after that
I also visualize the fluctuation of final concatenated file using last
100ns .gro using VMD. I found in my individual files the fluctuation of
ligand is different as compare to the final one.

So the concatenation of trr file is not proper what is the reason.

Please Help

With Regards
Neha Bharty

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