Re: Flat-bottom harmonic position restraints using colvars

From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Wed Feb 12 2020 - 19:24:22 CST

Hello,

Thanks to the response from Giacomo and David, the usage for harmonic walls
implemented with extrabonds is follows:
wall <atom> <atom> <k> <lower> <upper>

However, for my question, on applying position restraints to c-alpha atoms
with the harmonic wall potential, I am confused as to what should be the
second input to the atom index (when using with extrabonds). The first
input is the atom index for the c-alpha atom.

Thanks,
Daipayan

On Tue, Feb 11, 2020 at 5:12 PM Daipayan Sarkar <sdaipayan_at_gmail.com> wrote:

> 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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