Re: restrain lateral movement during ABF

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu May 17 2018 - 16:47:13 CDT

Hi Jerome,

thank you, I appreciate your help! I did not realize that it doesn't have
to be specific to the axis. My protein does not rotate, I use backbone
restrain for everything except the channel where I measure PMF.

My input file is below, does it look right? Also, do I understand it
correctly that in order to restrict the movement in the plane perpendicular
to distance colvar I have to use (1.0, 1.0, 0.0), while vertical movement
is restricted by distance colvar (i.e. I do not need to indicate
(1.0, 1.0, 1.0) in the distanceXY).

colvarsTrajFrequency 500
colvarsRestartFrequency 5000

colvar {
   name IonDistance

   width 0.1

   lowerboundary 70.0
   upperboundary 74.0

   lowerwallconstant 100.0
   upperwallconstant 100.0

   distance {
   oneSiteTotalForce
      group1 {
         atomnumbers { 66463 }
      }
      group2 {
         dummyAtom (1.485, -0.486, -0.418)
      }
   }
}

colvar {
   name distanceXY

   width 0.1

   lowerboundary 0.0
   upperboundary 5.0
   upperwallconstant 100.0

   distanceXY {
     ref {
    atomnumbers {dummyAtom (1.485, -0.486, -0.418) }
     }
     main {
      atomnumbers { 66463 }
     }

   axis(1.0, 1.0, 0.0)

  }
}

Thank you!

olga

abf {
  colvars IonDistance distanceXY
  fullSamples 500
  hideJacobian
}

On Thu, May 17, 2018 at 9:04 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> DistanceXY is just a name, it can function with any axis you choose (see
> the axis keyword).
>
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distanceXY
>
> If a fixed axis does not work because of overall protein rotation, you can
> make that a moving axis tied to the protein frame of reference.
>
> http://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvar_atom_groups_ref_frame
>
> Best,
> Jerome
>
>
>
> On 16 May 2018 at 23:34, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>
>> Hi all,
>>
>> I am trying to restrain lateral movement of the ion when it is just
>> outside the entrance of the channel during ABF calculations. My reaction
>> coordinate is the distance between the center of mass of the spherical
>> protein and the ion; it does not coincide with z axis, so I can't use
>> distanceXY. The protein is spherical, and the outer surface is convex. Is
>> there a colvar that I can use in such a case to keep the ion in place?
>>
>> If I were to make a tclBC script that would return the ion inside a
>> sphere of a small radius located just outside the entrance of the channel,
>> how would that affect ABF outcome for that window? Will such script
>> interfere with a similar script that I use to push out salt ions from
>> entering the channel?
>>
>> Thank you,
>>
>> Olga
>>
>
>

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