From: 林星雨 (linxingyu1986_at_gmail.com)
Date: Mon Jun 21 2010 - 04:17:57 CDT
I'm sorry I may have made a misconception about TI
Since protein is not scaled by lamda in TI for my system, its derivative
should be zero
Can anybody confirm my thinking now?
On Mon, Jun 21, 2010 at 11:26 AM, 林星雨 <linxingyu1986_at_gmail.com> wrote:
> Hi dear all,
> I have a question about NAMD TI
> It seems that in NAMD TI it can only calculate the derivatives of vdw and
> ele, but if I want to mutate a fragment of a ligand and for these two
> ligands they change the protein side-chain diherdral angle differently, then
> the free enegy change must be associated with this side-chain. So how can I
> use NAMD to get the free energy change?
> Many Thanks!
> Xingyu Lin
> National Institute of Biological Sciences, Beijing
> Dr. Niu Huang's Lab
> Tel: 80726688-8572
> Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East
> Road, NIBS B427
> Postcode: 102206
-- Xingyu Lin Currently: National Institute of Biological Sciences, Beijing Dr. Niu Huang's Lab http://www.nibs.ac.cn/ Tel: 80726688-8572 Address: Beijing ZhongGuanCun Life Science Park, NO.7 Science Park East Road, NIBS B427 Postcode: 102206
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