Hello,
As far as I am aware, there are no plans to incorporate the string method
in Amber. If and other developers are working on this, they will most
likely let you know.
The nudged elastic band method can be used for conformational changes in
large systems, depending on what you mean by large. I have used it to look
at minimum potential energy paths for base flipping in a protein-DNA
complex (Bergonzo et al. JACS 2011). This system size was a 273 residue
protein + 16 base pair DNA in TIP3P solvent, totaling ~60,000 atoms.
Hope this is helpful,
-Christina
On Thu, Nov 1, 2012 at 7:49 AM, Tan Yaw Sing <tanys.bii.a-star.edu.sg>wrote:
> Hi Amber users,
>
> Are there any plans to include the string method to find minimum free
> energy paths (Vanden-Eijnden, Phys Rev B, 2002) in future versions of
> Amber, and if so, is there a working version of the program already? I
> am currently trying out the nudged elastic band method but it is not
> as widely implemented as the string method, and as far as I know, it
> has not been applied to large proteins yet.
>
> -Yaw Sing
>
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>
--
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Christina Bergonzo, PhD
Postdoctoral Fellow
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Office: Biopolymers Room 295
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Nov 01 2012 - 07:30:06 PDT
