Re: Colvars Orientation Question

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Jul 03 2019 - 03:49:55 CDT

Hi Alexander,

the explanation to this mystery might be in the colvars.traj file. Look in
particular for the initial and final values of the orientation quaternion.

Jerome

On Tue, 2 Jul 2019 at 23:50, Xander Gonzalez <xandergonz1_at_gmail.com> wrote:

> 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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