[gmx-users] Hamiltonian replica exchange

[marcos]

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: arloa at mail.fcq.unc.edu.ar
> > To: gmx-users at gromacs.org
> > 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 gmx-users at gromacs.org
> > 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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 
> ______________________________________________________________________
> Express yourself instantly with MSN Messenger! MSN Messenger
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php