FEP configuration file

From: List (zheng042003_at_yahoo.com)
Date: Mon Jan 28 2008 - 10:55:21 CST

Dear NAMD/FEP experts,

I have some questions about FEP.

1) Before the production FEP run, should the hybrid structure be minimized at T=0, heated to 300, and then equilibrated at 300?

2) When I run the heating, the job died with error message of "Constraint failure in RATTLE algorithm for atom XXX" where XXX is the number of an CB atom on the to-be-mutated hybrid residue. The only constraint I have in heating is on C alpha which seems to be necessary. Is there anying wrong in my setting?

3) For the FEP production run, the configuration file I have is the combination of a regular production-run plus the FEP portion from FEP tutorial. Is this the right way to do it?

Many thanks,


Never miss a thing. Make Yahoo your homepage.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:52 CST