AMBER Archive (2004)

Subject: AMBER: Free energy in Amber8

From: Jiten (
Date: Tue Jun 01 2004 - 05:11:54 CDT

Dear Amber users,

I am a bit confused is setting the input file for Free energy using thermodynamics intergration in sander (amber8). Am I going to run idependent MD's with diffferent clamda values for the choice of my n-values. For the MD of the next clamda - should start from the restart file of the previous clamda value? Or is it possible to combine in one input file? Can anybody provide me a sample input file for the same.

One futher question - how much time for the MD is generally considered to be good for each of the clamda vales. (say 100 ps etc) ?

Thanking you in advance?

N. Jiten Singh
C/O Prof. Kwang S. Kim
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab ) / 279-4138 ( Appt )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : and
Home Page :

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to