Re: Binding free energy tutorial

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Sat Oct 27 2018 - 03:15:30 CDT

Dear Jing Liang,

Please try running that part of the tutorial again with the most recent NAMD 2.13b2. The "misunderstanding" between the tutorial configuration file and the Colvars module has recently been fixed.

Best regards,
Dave

--
David J. Hardy, Ph.D.
Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Ave., Urbana, IL 61801
dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
> On Oct 27, 2018, at 3:37 AM, jing liang <jingliang2015_at_gmail.com> wrote:
> 
> Hi,
> 
> I downloaded the tutorial "Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations" in the site: https://www.ks.uiuc.edu/Training/Tutorials/ <https://www.ks.uiuc.edu/Training/Tutorials/>
> The Alchemical Bound state simulation only ran fine for the backwards direction. In the forwards
> direction it showed the following error: jacobi too many iterations.  I am working with the 
> version 2.12 shared memory version. Have you experienced this issue in the present test case? 
> 
> Thanks.
> 
> 

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