[gmx-users] Hamiltonian replica exchange
arloa at mail.fcq.unc.edu.ar
Thu Oct 16 00:13:25 CEST 2008
On Wed, 2008-10-15 at 10:43 +0200, Berk Hess wrote:
> 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.
The idea of backbone torsional bias is from Kannan and Zacharias
They fold peptides with only 5-7 replicas.
> 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.
> > 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.
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