Re: Flat-bottom harmonic position restraints using colvars

From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Tue Feb 11 2020 - 16:12:12 CST

Hi Dave, Giacomo,

Many thanks for your help and message. I will try this new feature and let
you all know how it goes.
More soon.

Best regards,
Daipayan

On Tue, Feb 11, 2020 at 4:58 PM David Hardy <dhardy_at_ks.uiuc.edu> wrote:

> Hi Daipayan,
>
> Sorry, I just now saw this exchange.
>
> The harmonic wall potential was added in December. You can get it by
> downloading the nightly build. In the included user documentation, the
> section discussing extra bonds explains the use of this "wall" potential.
>
> 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 Feb 10, 2020, at 8:41 PM, Daipayan Sarkar <sdaipayan_at_gmail.com> wrote:
>
> Hi Giacomo,
>
> Sorry for the late reply. Thanks for your explanation. I have modified
> the range, such that all values are positive.
> Second, I performed two separate simulations, keeping one harmonic wall
> restraint on at a time, and it works.
> Finally, for my original question, I did not get any feedback on how to
> implement the harmonic wall potential with extrabonds (based on the link
> you shared).
>
> Best Regards,
> Daipayan
>
>
>
> On Mon, Feb 10, 2020 at 7:14 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi Daipayan, first of all there is no need to specify the lowerWalls (or
>> lowerWallConstant, for that matter) if these are well below the possible
>> range of values: in this case, a distance variable can never go below -2 Å.
>>
>> Secondly, the MISC column reports values of the restraint energy for all
>> variables combined (plus, many other kinds of restraints than Colvars ones,
>> if you have them). So for a frame where d1 is within range, you could
>> still get a positive MISC energy from d2. Looking at some of the highest
>> points in your plots, this seems to be the case.
>>
>> Lastly, your original question was about applying flat-bottom restraints
>> on individual atoms, which is a bit different with what you are doing here.
>>
>> Did you get any feedback regarding the new per-atom flat-bottom restraint
>> feature? The NAMD development team is copied also.
>>
>> Giacomo
>>
>> On Sun, Feb 9, 2020 at 1:07 PM Daipayan Sarkar <sdaipayan_at_gmail.com>
>> wrote:
>>
>>>
>>> Hello,
>>> This is a follow-up on our recent discussion for the flat-bottom
>>> harmonic potential implemented as part of collective variables. To
>>> validate, if the potential is indeed flat-bottom harmonic as documented: (
>>> https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_harmonic_walls),
>>> I applied this to the tma-aco example with the following protocol.
>>>
>>> The harmonic walls potential are applied between dummyatoms (x,y,z
>>> coordinates of the center of mass) and their respective molecules, tma and
>>> aco. The two distances d1 (dummyatom and tma) and d2 (dummyatom and aco)
>>> written to the colvars.traj file are plotted against the MISC term in the
>>> log file (the two plots are attached). Each point in the scatter plot is a
>>> value from the trajectory every 1000 steps. The result shows that the MISC
>>> potential is flat-bottom (in-shape), however, there are points within the
>>> cut-off value of 2, set for the upper wall, which have a non-zero value for
>>> the potential. Switching off colvars has the MISC term go to zero, which
>>> confirms the MISC term is entirely from the harmonic walls restraint
>>> potential. Please help me understand why some values, within the harmonic
>>> walls have a non-zero value.
>>>
>>> Thanks for your help.
>>>
>>> Following, is my colvars script:
>>>
>>> colvars on
>>> cv config "
>>> colvarsTrajFrequency 1
>>> colvarsRestartFrequency 1000
>>> colvar {
>>> name d1
>>> distance {
>>> group1 {
>>> dummyAtom (-4.317, -0.383, 0.141)
>>> }
>>> group2 {
>>> atomNumbersRange {1-17}
>>> }
>>> }
>>> }
>>> "
>>>
>>> cv config "
>>> colvarsTrajFrequency 1
>>> colvarsRestartFrequency 1000
>>> colvar {
>>> name d2
>>> distance {
>>> group1 {
>>> dummyAtom (0.360, 0.03, 0.405)
>>> }
>>> group2 {
>>> atomNumbersRange {18-27}
>>> }
>>> }
>>> }
>>> "
>>>
>>> cv config "
>>> harmonicWalls {
>>> name hw1
>>> colvars d1
>>> lowerWalls -2.0
>>> upperWalls 2.0
>>> lowerWallConstant 2.0
>>> upperWallConstant 2.0
>>> }
>>> "
>>>
>>> cv config "
>>> harmonicWalls {
>>> name hw2
>>> colvars d2
>>> lowerWalls -2.0
>>> upperWalls 2.0
>>> lowerWallConstant 2.0
>>> upperWallConstant 2.0
>>> }
>>> "
>>>
>>> Best Regards,
>>> Daipayan
>>>
>>> ---------- Forwarded message ---------
>>> From: Daipayan Sarkar <sdaipayan_at_gmail.com>
>>> Date: Wed, Feb 5, 2020 at 2:34 PM
>>> Subject: Re: namd-l: Flat-bottom harmonic position restraints using
>>> colvars
>>> To: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>>> Cc: NAMD list <namd-l_at_ks.uiuc.edu>, <dhardy_at_ks.uiuc.edu>
>>>
>>>
>>> Hello Giacomo,
>>> Many thanks for your quick response and sharing the link. After
>>> checking, harmonic wall potential is available through extrabonds. The NAMD
>>> documentation takes me to v2.13, where the usage of this new feature is not
>>> listed (standard harmonic potential for extrabonds).
>>>
>>> Can you or David (copying him here) help me with the usage of this
>>> feature, especially for the part "BondValue now has an additional parameter
>>> representing the upper wall."
>>>
>>> Thank you again,
>>> Daipayan
>>>
>>> On Wed, Feb 5, 2020 at 1:51 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>>> wrote:
>>>
>>>> Hello Daipayan, those would work on the collective variables (i.e. one
>>>> or a few numbers for the entire system) as opposed to an entire set of
>>>> Cartesian coordinates. And in any case, it would be quite inefficient to
>>>> run a multitude of restraints via Colvars if they d don't need a collective
>>>> operation.
>>>>
>>>> Check out the nightly build, because a similar feature for Cartesian
>>>> coordinates has just been added:
>>>> https://charm.cs.illinois.edu/gerrit/c/namd/+/5316
>>>>
>>>> On Wed, Feb 5, 2020 at 1:29 PM Daipayan Sarkar <sdaipayan_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> My objective is to apply flat-bottom harmonic position restraints to
>>>>> the C-alpha (CA) atoms. To achieve this, I am using the colvars
>>>>> harmonicWalls. I have a question regarding setting the values of lower and
>>>>> upperWalls, with respect to the reference CA positions.
>>>>>
>>>>> Typically, a regular harmonic position restraint is applied, where a
>>>>> reference PDB is provided as an input to the parameter consref. My
>>>>> question, is can we pass a reference pdb to colvars and set the upper
>>>>> and lower bounds with respect to the selection?
>>>>>
>>>>> Following is my colvar definition. Any help is greatly appreciated.
>>>>>
>>>>> #########################
>>>>> colvars on
>>>>> colvarsTrajFrequency 100
>>>>>
>>>>> cv config "
>>>>> colvar {
>>>>> name calpha
>>>>> group1 {
>>>>> psfSegID AP1
>>>>> atomNameResidueRange CA 1-76
>>>>> }
>>>>> }
>>>>> "
>>>>>
>>>>> cv config "
>>>>> harmonicWalls {
>>>>> name fb_restraint
>>>>> colvars calpha
>>>>> lowerWalls * #add_lower_bound_from_ref_CA_position*
>>>>> upperWalls *#add_upper_bound_from_ref_CA_position*
>>>>> lowerWallConstant 10.0
>>>>> upperWallConstant 10.0
>>>>> }
>>>>> "
>>>>> #########################
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Daipayan
>>>>>
>>>>
>>>>
>>>> --
>>>> Giacomo Fiorin
>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>> Research collaborator, National Institutes of Health, Bethesda, MD
>>>> http://goo.gl/Q3TBQU
>>>> https://github.com/giacomofiorin
>>>>
>>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Research collaborator, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>

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