Hi,
> I performed MD simulation using pmem.cuda (AMBER 2011 package) on GPU
> workstation and found that trajectory does not stabilized even after
> 10ns.
> the details are as follows :
at first glance your output rmsd plots do not look unusual to me. The rmsd
hits a value of about three, stops rising and oscillates there. What do
you think the plot should look like? It depends on your system, but you
will never see a complete 'flat' rmsd curve, since your system continues
to explore conformational space. It is hugely dependent on your simulation
conditions and starting structure, but seeing a macromolecular rmsd of ca.
3 A for a solvated protein may be expected. You will have to do much more
analysis to get a better feel of what is really going on in your system,
i.e. visualization, clustering analysis, 2D-rmsd and longer simulation
runs are the first ideas that come to mind.
Kind Regards,
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Jan 17 2012 - 07:00:03 PST
