Tutorial-l Mailing List

From: Alexander Gonzalez (acgonzalez_at_uchicago.edu)
Date: Mon Jul 01 2019 - 14:29:07 CDT

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!

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