Hi,
the equilibration procedure you mention seems reasonable to me. Just to
check:
> completion of min2 step, the last coordinates of restart files were
> 0.0000.
The last line in your restart file are the box dimensions, which should
not be zero. Note that rst-files save coordinates first, followed by 3N
velocities, so if the last half of the rst-file is all zeroes, this
corresponds to a 0K structure (which is ok after minimization)
> temp=3000.0,
^^^^^^^^^^^^
typo or are you really simulating at 3000K?
> After completion of every job the coordinates of restart files were
> reducing to 0.
I am not sure what you mean here. The coordinates should change after each
run. Visualize your system to check if something actually changes.
> System is not getting equilibrated even after 2ns run , RMSD is increasing
> to 3angstorm, can i proceed with same to run production run.
2 ns may not be enough to fully equilibrate a protein structure. Be
prepared to run (much) longer for a stable rmsd. But also check what is
happening in your structure, maybe the rmsd is only driven by a flexible
tail that is non-functional.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Sep 22 2010 - 03:00:03 PDT
