Re: Binding free energy tutorial

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun Oct 28 2018 - 10:20:50 CDT

Hi everyone, I can confirm that the message:
colvars: Error: lower wall and upper wall are equal in the domain of the
variable "Psi".
is obtained correctly, because -180° and 180° are the same angle. In much
older versions, the Colvars walls code was simpler and it was possible to
resolve the error internally by disabling the walls.

The improved version does not allow this as easily, and most importantly we
agreed during earlier private conversations that an error message is more
appropriate than a warning about incorrect input. The tutorial's input is
wrong most likely due to inadvertently pasting the input for a Psi interval
shorter than -180°:180°: this is a type of mistake that we all do often,
but it is easy to fix by disabling the walls.

Jing, please disable the wall potentials for that example, and that will
resolve your error. For more information about the very few example of
syntax changes, this is the relevant section:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_config_changes

Giacomo

On Sat, Oct 27, 2018 at 4:35 PM David Hardy <dhardy_at_ks.uiuc.edu> wrote:

> 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 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.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> El sáb., 27 oct. 2018 a las 10:15, David Hardy (<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, 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/
>> 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.
>>
>>
>>
>>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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