Re: Binding free energy tutorial

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Sat Oct 27 2018 - 15:34:24 CDT

Let's please keep our replies on the list.

I thought that Giacomo and Jerome had updated Colvars to still maintain backwards compatibility with the tutorial's older syntax for defining a harmonic collective variable, but maybe I'm mistaken. (Hey, if either of you see this, maybe respond?)

At any rate, the issue is then not a bug in the code (it seems to be giving a correct error message) but instead a bug in the tutorial. For now, you can solve this one yourself by taking a look at the Colvars chapter in the NAMD user guide to find out how to correctly define a "harmonicwalls" collective variable and then fixing the config file.

You'd be doing everyone involved a favor if you reply to namd-l with the fixed syntax.

Thanks.

--
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 28, 2018, at 3:35 AM, jing liang <jingliang2015_at_gmail.com> wrote:
> 
> Hi, 
> 
> thanks for your comments. I downloaded the 2.13b2 KNL version from ks.uiuc.edu <http://ks.uiuc.edu/> website. It doesn't show the 
> message I wrote before. Instead it says that the lower and upper wall values are the same for the angles:
> 
>  colvars:   Initializing a new "harmonicwalls" instance.
> colvars:   # name = "Psiw"
> colvars:   # colvars = { Psi }
> colvars:   # outputEnergy = off [default]
> colvars:   # timeStepFactor = 1
> colvars:   # writeTISamples = off [default]
> colvars:   # writeTIPMF = off [default]
> colvars:   # forceConstant = 1 [default]
> colvars:   # targetForceConstant = -1 [default]
> colvars:   # lowerWalls = { -180 }
> colvars:   # upperWalls = { 180 }
> colvars:   # lowerWallConstant = 0.5
> colvars:   # upperWallConstant = 0.5
> colvars: Error: lower wall and upper wall are equal in the domain of the variable "Psi".
> FATAL ERROR: Error in the collective variables module: exiting.
> 
> I don't get that error message if I use instead of -180 the value of -179.999 but I guess that could be a bug from
> the code which might have other consequences?
> 
> Thank you.
> 
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> El sáb., 27 oct. 2018 a las 10:15, David Hardy (<dhardy_at_ks.uiuc.edu <mailto:dhardy_at_ks.uiuc.edu>>) escribió:
> 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 <mailto:dhardy_at_ks.uiuc.edu>, http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/~dhardy/>
> 
> 
>> On Oct 27, 2018, at 3:37 AM, jing liang <jingliang2015_at_gmail.com <mailto: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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