RE: AMBER: Free energy for part of the system

From: jialei <>
Date: Wed, 5 Dec 2007 01:10:18 +0000

Dear Dave,
Yes. The target and control have same sequences. Actually they have same set of atoms so that I can compare them. But their comformations are different.We want to study the contribution to free energys from different conformations.
Thank you so much for the help.
> Date: Tue, 4 Dec 2007 10:37:16 -0800> From:> To:> Subject: Re: AMBER: Free energy for part of the system> > On Tue, Dec 04, 2007, jialei wrote:> > > > We would like to compare free energies between two> > duplexes (one target duplex and one control). The reason why we thought out> > computing the central 5mer free energy is that there are end effects during> > the simulation, while the central 5mer looks normal.> > Do the target and the control have the same sequence? If not, I don't see how> you can make a meaningful free energy comparison. And if they do have the> same sequence (so that the differences are in the non-central base pairs), I> don't see how you would interpret the result (although you could certainly> calculate it in the manner you suggest).> > ...regards...dac> > -----------------------------------------------------------------------> The AMBER Mail Reflector> To post, send mail to> To unsubscribe, send !
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Received on Wed Dec 05 2007 - 06:07:35 PST
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