Re: Multiple Constraints Equilibration

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 01 2019 - 11:56:53 CST

In this particular case, it may be simplest to use Colvars restraints on
the COM and the orientation of the ligand (see examples).

With the ligand being small, there is not much to gain from parallelizing
the restraints over nodes via tclBC, so the extra effort of writing a
correct Tcl script and the computational overhead may not be worth it.

Giacomo

On Fri, Mar 1, 2019 at 12:29 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> To my knowledge the "constraints" keyword is all or none. Depending on
> your atom selection, I'm not entirely sure a z-coordinate only restraint on
> your ligand would be much different from all coordinates.
>
> You might try a TclBC force on your ligand instead.
>
> HTH,
> BKR
>
> On Thu, Feb 28, 2019 at 8:33 PM McGuire, Kelly <mcg05004_at_byui.edu> wrote:
>
>> Is it possible to have multiple harmonic constraints during
>> equilibration? I would like to constrain the XYZ coordinates of my
>> protein, but only constrain Z for my ligand. Right now I use the code
>> below, but not exactly sure how to modify it so that only the z-coordinates
>> for the ligand are constrained. I found selectConstrZ, but it's not very
>> specific in only certain atoms can have this applied and not others.
>>
>>
>> constraints on
>> consref Minimization_restraints.pdb
>> conskfile Minimization_restraints.pdb
>> constraintScaling 2
>> consexp 2
>> conskcol B
>>
>>
>>
>> *Kelly L. McGuire*
>>
>> *PhD Candidate*
>>
>> *Biophysics*
>>
>> *Department of Physiology and Developmental Biology*
>>
>> *Brigham Young University*
>>
>> *LSB 3050*
>>
>> *Provo, UT 84602*
>>
>>
>>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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