From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 10 2020 - 06:14:11 CST
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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