On Wed, 2008-10-15 at 10:43 +0200, Berk Hess wrote: > Hi, > > What do you mean exactly with Hamiltonian replica exchange? >
I would like to do H-RexMD with backbone torsional bias, as an alternative to T-RexMD for peptide folding. Each replica run at the same Temp but with a different force field. The replicas are exchanged according to Delta = beta [ En(Xm) - Em(Xm) + Em(Xn) - En(Xn) ] if the energy on every replica differs only by a torsional potential bias V(X) scaled by f(i) in every replica i, En(Xm) - Em(Xm) = [f(n) - f(m)] V(Xm) and Delta = beta [f(n) - f(m)] [V(Xm) - V(Xn)] This is eq. 8 in Affentranger et. al. http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2006/2/i02/abs/ct050250b.html The idea of backbone torsional bias is from Kannan and Zacharias http://www.ncbi.nlm.nih.gov/pubmed/17120231 They fold peptides with only 5-7 replicas. Saludos, Marcos. > There is a (hidden) implementation of Hamiltonian exchange > for the free energy coupling parameter lambda in 4.0. > This uses delta_lambda*dH/dlambda iso delta_H, > which is why it is hidden. > In 4.1 we will use delta_H. > > Berk > > > > > ______________________________________________________________________ > > From: [EMAIL PROTECTED] > > To: [email protected] > > Date: Tue, 14 Oct 2008 14:20:55 -0300 > > Subject: [gmx-users] Hamiltonian replica exchange > > > > Hi, > > > > Is Hamiltonian replica exchange implemented in gmx 4.0? > > can't find it in the manual. > > > > Marcos. > > > > > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > ______________________________________________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
