[gmx-users] Different fluctuation after concatenation

Justin Lemkul jalemkul at vt.edu
Wed Nov 12 13:50:43 CET 2014

On 11/12/14 4:30 AM, neha bharti wrote:
> 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
> step.
> 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.

Concatenation does not change coordinates.  If there is something wrong, you 
will have to quantify it, because your description isn't very clear.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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