Re: How to do FEP simulations to calculate the absolute free energy of solvation?

From: Jérôme Hénin (
Date: Sat Nov 15 2003 - 04:27:35 CST


In case you didn't know, there is a tutorial for alchemeical FEP available at

Anyway, the setup may be a little complex in the beginning. What do you want
to compute exactly ? I'm not sure I understand what you mean by "absolute
free energy of a molecule". If you mean the free energy of creation of the
molecule in vacuum, it is likely to be force-field dependent and not to have
much physical meaning.


> Dear namd users,
> Recently I wanna to do some research on the absolute free energy of some
> small organic molecules using the FEP in NAMD. But I get in the trouble in
> how to begin it.
> From the manual I know NAMD using dual topologies to do FEP. So one must
> define the dual topologies in the PDB file. But I don't know how to define
> the PDB file. Does anyone have any experience to do it. Could you send me a
> example of the files you use to do simulations.
> For a example, I want to do the calculations on CH4. How to define to files
> used to do simulation?
> Thank you in advance.
> Sincerely yours
> ----
> PeiQuan Chen
> ________________________________________________________________________
> PeiQuan Chen Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone: (86)2223507510 Mobile Phone: (+86)13920675030
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:08 CST