Re: [AMBER] Enquiry about tutorial A5 - section 7 on nudged elastic band calculation

From: Christina Bergonzo <cbergonzo.gmail.com>
Date: Tue, 5 Oct 2010 09:59:14 -0400

Hi,

The data used here is the phi/psi angles along the transition path, which
were taken from the VMD image or can be calculated using ptraj.
The potential energy surface was generated by restrained energy minimization
of alanine dipeptide at 2 degree intervals over phi/psi space.

-- 
Christina Bergonzo
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Doctoral Student, Simmerling Lab
Center for Structural Biology
CMM Bldg, Room G90
Stony Brook University
Stony Brook, NY 11794-5115
Tel. 631-632-1560
Web: http://comp.chem.sunysb.edu
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
On Mon, Oct 4, 2010 at 5:12 PM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I am following the tutorial A5 to do Nudged Elastic Band calculation.
>  However, I am wondering how to generate a diagram like the last figure in
> TUTORIAL A5 - SECTION 7
>
>
>
> What is the data used to generate this diagram?
>
>
>
> Best regards,
>
>
>
> many thanks
>
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Received on Tue Oct 05 2010 - 07:00:09 PDT