AMBER Archive (2008)

Subject: AMBER: Accessing Equilibration Results

From: dpandit_at_brandeis.edu
Date: Thu Apr 17 2008 - 08:29:35 CDT

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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu