From: PQCHEN (namd_at_eyou.com)
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
namd_at_eyou.com
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