AMBER Archive (2009)

Subject: [AMBER] PMF calculation

From: Arnaud (arnaud_at_lcc-toulouse.fr)
Date: Tue Feb 17 2009 - 12:10:18 CST


Dear Amber users,

I perfomed three time the same PMF calculation on the same complex (a drug
and receptor) but using amber8, amber9 and amber10. In each case, PMF was
evaluated from the WHAM post-processing. For all my calculations parameters
were strictely the same (same condition, same time simulation, same windows,
same constraint force, ...)

For all simulations, dissociation pathways were similar but PMF values
obtained with amber8 were twice those obtained with amber9 or amber10.

Where is the mistake ?

Thanks very much.

Philippe

-------------------------------------------
Laboratoire de Chimie de Coordination/CNRS

___________________________________________________________________
CNRS / Laboratoire de Chimie de Coordination

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

_______________________________________________ AMBER mailing list AMBER_at_ambermd.org http://lists.ambermd.org/mailman/listinfo/amber