Re: Flat-bottom harmonic position restraints using colvars

From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Mon Feb 10 2020 - 20:41:47 CST

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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