Re: Binding free energy tutorial

From: jing liang (jingliang2015_at_gmail.com)
Date: Wed Nov 07 2018 - 08:17:44 CST

Hi,

I downloaded the binding free energy tutorial and it seems there have been
some changes to the files
for instance a parameter numMinSteps which was not there some weeks ago
(maybe I am wrong).
When I run the namd scripts for forward and backward systems it throws the
following error using
different versions (2.12b and 2.13b):

ERROR: 'alchLambda' is a required configuration option
ERROR: when 'alch' is set
ERROR: alchLambda defines: Coupling parameter value
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: runFEPmin

El mié., 31 oct. 2018 a las 10:31, jing liang (<jingliang2015_at_gmail.com>)
escribió:

> Hi everyone,
>
> I ran the binding free energy tutorial case (alchemical route) with the
> suggested modifications. For the unbound simulation
> I got the BAR estimator of -54.12 and for the bound case this estimator
> was -36.41. That BAR estimator was obtained through
> the parseFEP plugin from VMD. By looking at the summary.png plot from
> parseFEP, I noticed that the forward and backward
> pathways (in both bound and unbound cases) show a larger hysteresis
> (~10kcal/mol difference) than the one you presented
> in the Fig. 5 of the tutorial. I got some questions, any comment is
> appreciated:
>
> * Are all energy restraints included in the BAR estimator? I mean, for
> instance the free energy contribution due to the restraining
> potential as in Fig. 7 of the tutorial. Or should I get the energy
> contribution by integrating some extra terms?
>
> * In the tutorial it says that one can do "grep dA/DLambda rest-01.log" to
> get the restraints contributions, but I couldn't find that
> output file.
>
> * Should the binding free energy difference be equal to the (BAR estimator
> unbound) - (BAR estimator bound)?
>
> Thanks.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> El dom., 28 oct. 2018 a las 17:47, David Hardy (<dhardy_at_ks.uiuc.edu>)
> escribió:
>
>> 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
>>
>> 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
>>
>>
>>

This archive was generated by hypermail 2.1.6 : Sun Dec 08 2019 - 23:20:15 CST