From: Daipayan Sarkar (sdaipayan_at_gmail.com)
Date: Wed Feb 05 2020 - 13:34:38 CST
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
>
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