Re: Colvars Orientation Question

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Jul 01 2019 - 19:01:39 CDT

Hi Alex, it is likely that the combined effect of the two rotations that
you are applying is inducing a torque on the entire protein. Can you try
first to see if a static harmonic restraint is stable for this choice of
variable before starting to move it?

Giacomo

On Mon, Jul 1, 2019 at 4:01 PM Alexander Gonzalez <acgonzalez_at_uchicago.edu>
wrote:

> Hello,
>
> I've been trying to run a simulation on a new structure with orientation
> collective variables to separate two portions of a protein (resid 43-515
> and resid 542-1011), I followed the "Exploring Complex Conformational
> Transition Pathways" tutorial, using the provided orientation.tcl to find
> the orientation quaternions. I changed the colvars.conf file as is shown
> below:
>
> #############################################################
> ## Collective Variables ##
> #############################################################
>
> # Global parameters
> colvarsTrajFrequency 500
>
> colvar {
> name d1_2
> orientation {
> atoms {
> psfSegID AP1
> atomNameResidueRange { CA 43-515 }
> }
> refPositionsFile CC-complete-model-ChainA-solvate-centered-mini-LF.pdb
> }
> }
>
> colvar {
> name d3_4
> orientation {
> atoms {
> psfSegID AP1
> atomNameResidueRange { CA 542-1011 }
> }
> refPositionsFile CC-complete-model-ChainA-solvate-centered-mini-LF.pdb
> }
> }
>
> harmonic {
> name harm
> colvars { d1_2 d3_4 }
> # initial values
> centers { ( 1 , 0 , 0 , 0 ) ( 1 , 0 , 0 , 0 ) }
> # target values
> targetCenters { ( 0.984807753012208 , -0.009832450473359431 ,
> 0.04197699686335437 , 0.16821101136975466 ) ( 0.984807753012208 ,
> 0.009832450473359431 , -0.04197699686335437 , -0.16821101136975466 ) }
> # force constant in kcal/(mol*rad^2)
> forceConstant 10000
> # steering protocol time
> targetNumSteps 200000
> # calculate work
> outputAccumulatedWork on
> }
>
> The resulting simulation seems to separate the two protein sections, but
> not before rotating and distorting the protein for the first few frames. I
> also tried accomplishing this separation with the spin colvars, where I
> used the axis.tcl script to get the principal axes. Drawing these axes
> seems to show that they are accurate for the rotation that I want to
> accomplish. Despite this, the spin colvar simulation also leads to the
> structure rotating and distorting in unwanted ways for the first few frames
> of the simulation before separating as expected. I would really appreciate
> advice for possible things to try regarding this, also let me know if you
> want more information about the specific structure/simulation I am
> attempting. Thanks for your time!
>

-- 
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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