Re: Colvars Orientation Question

From: Xander Gonzalez (xandergonz1_at_gmail.com)
Date: Tue Jul 02 2019 - 16:46:11 CDT

Thank you for the feedback, I have been trying to run a static harmonic
restraint and running into some trouble. I have tried setting targetCenters
to the same as Centers as well as not using targetCenters at all. Both
result in the protein making what seems to be a complete rotation. Setting
forceConstant as 1 seems to result in a static protein, but I am not sure
if this is correct. Did you have any specific ideas about how to create a
static harmonic restraint? Or do the results that I have been getting imply
something about the system?

Thank you again,
Alexander

On Mon, Jul 1, 2019 at 7:02 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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