[gmx-users] Different fluctuation after concatenation
nehabharty123 at gmail.com
Wed Nov 12 10:30:08 CET 2014
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.
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