Hi All:
I am following guidelines suggested in AMBER tutorials to conduct
equilibration. After running 20PS of NVE, I switched to 200 PS of NPT.
It is suggested that Energy(Total, Kinetic & Potential), Temperature,
Volume, Density,Pressure and RMSD should be checked. My all values
except pressure and RMSD values appear stable. I came to know for the
list that pressure does fluctuate and it is OK. When I checked AMBER
archive for RMSD values, there are different opinions about it. I am
not sure how much RMSD is acceptable before submitting the production
run. I calculated RMSD of CA atoms of the protein. I have following
questions:
Is RMSD of 2 - 2.5 A is acceptable?(For HIV loop tutorial, RMSD is
smooth and less than 1 A)
Is it worthwhile to perform long (about 600 PS compared to 200 PS)
equilibration run before submitting the production run.
Thanks,
Deepa
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Received on Fri Apr 18 2008 - 21:20:04 PDT
