Jarzynski equality and the pull direction in SMD

From: Paulo Cesar Telles de Souza (paulocts_at_gmail.com)
Date: Thu Apr 02 2009 - 19:00:40 CDT

Dear all,

I have a doubt about the aplication of SMD simulations to obtain binding
free energy using the Jarzynski Equality: Does the pull direction have to be
the same in all the SMD trajectories, but with different initial
configurations, or should I vary the pull directions in order to have a
bigger sample of ways of occurring a process?

In my study I try to obtain the binding free energy of ligant that is docked
in the surface of a receptor. I think that the reaction coordinate is almost
the same if I change a little the pull direction, but I did not find any
requirement in Jarzynski Equality theory saying that the sample of work has
to be composed by SMD simulations of only one pulling direction.

Can anyone help me ?

Best regards

Paulo Cesat Telles de Souza
Campinas State Universiy
Brazi

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