From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Mar 25 2009 - 17:51:17 CDT
Do you need an alchemical change that "causes" a conformational change, or just a conformational change evaluated? If just the free energy of a conformational change (and not the free energy of alchemical change) needs to be calculated I would suggest strongly that you download the new beta version of namd (namd2.7b1) and use either Adaptive Biasing Force or Metadynamics (both described in the new manual under the "Collective variables" section) to calculate the free energy change of your system. If there is also an alchemical change to be calculated, we can offer suggestions how you might best proceed, but your email sounds like you are interested in the conformational free energy change.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 Lixia Jin Day <ljin12_at_asu.edu> writes: > Date: Wed, 25 Mar 2009 13:21:19 -0700 > From: Lixia Jin Day <ljin12_at_asu.edu> > To: namd-l_at_ks.uiuc.edu > Subject: namd-l: Free energy of conformational change > Return-Path: char_at_halifax.ks.uiuc.edu > Message-ID: <f7c18c850903251321o3312d82i119865796104e559_at_mail.gmail.com> > X-Spam-Status: No, score=-1.8 required=5.0 tests=BAYES_00,HTML_00_10, > HTML_MESSAGE autolearn=no version=3.1.7-0+tcb1 > > In the FEP section of the user's guide, it says:" The system is efficient if > only a few coordinates, either of individual atoms or centers of mass of > groups of atoms, are needed." > > Here I have two conformations of a protein (about 300aa), can I calculate > the free energy changes during the transition from one conformation to > another? > Thanks! > > Lixia
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:31 CST