From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Mar 01 2007 - 11:40:00 CST

On Thu, 1 Mar 2007, Shulin Zhuang wrote:

dear shulin,

first of all, i suggest you pay a little more attention to
how and where you post request. e.g. write a more careful message
that contains all your questions and send it to the right mailing
list (i.e. the NAMD list and not the VMD list).

SZ> How to calculate the free energy change? I do not know how to do it. Wish
SZ> you can give me any suggestions or recommend me some papers.

your question is very unspecific and you don't state how much background
in free energy methods you have. in case of none, i would suggest you
start with a textbook on a very simple example (preferably on
umbrella sampling, which is expensive but considered very accurate),
and then move on to less time consuming but more approximate methods,
where you need to know what you are doing.

there are some examples, even tutorials referenced on the namd homepage.

please ask again, if you are more clear about _what_ you
want to do and where your problems are.

cheers,
   axel.

SZ> Great thanks.
SZ>
SZ>
SZ> On 3/1/07, Shulin Zhuang <shulin.zhuang_at_gmail.com> wrote:
SZ> >
SZ> > Dear All,
SZ> >
SZ> > Here, Can the NAMD is used to evaluate the free energy of lipid/protein
SZ> > interacion in biological membranes? If can, How to do that? Great thanks
SZ> > for the suggestions.
SZ> >
SZ> > Best wishes
SZ> > shulin
SZ> >
SZ> > --
SZ> > Shulin Zhuang
SZ> > Chemistry Department
SZ> > Zhejiang University PRC
SZ> > shulin.zhuang_at_gmail.com
SZ> >
SZ>
SZ>
SZ>
SZ>

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
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If you make something idiot-proof, the universe creates a better idiot.