Re: Binding free energy tutorial

From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Sun Oct 28 2018 - 11:47:37 CDT

Hi Giacomo,

Thanks for clarifying. Sorry for my misunderstanding about how Colvars was now handling this configuration.

I will get in touch off-list with the tutorial authors.

Best regards,
Dave

> On Oct 28, 2018, at 11:20 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> 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 <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 <mailto: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 <mailto:dhardy_at_ks.uiuc.edu>, http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/~dhardy/>
>> On Oct 28, 2018, at 3:35 AM, jing liang <jingliang2015_at_gmail.com <mailto: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.
>>>
>>>
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU <http://goo.gl/Q3TBQU>
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>

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