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

From: PQCHEN (
Date: Fri Nov 14 2003 - 22:24:01 CST

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

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