Re: restrain lateral movement during ABF

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu May 17 2018 - 17:06:02 CDT

Keep in mind that the components of the axis vector are not logical flags:
they indicate the direction of the axis, to which the plane is orthogonal.
Normalization aside, the two vectors that are orthogonal (1, 1, 0) are: *(1,
-1, 0)* and *(0, 0, 1)*. Is this the plane you want?

Giacomo

On Thu, May 17, 2018 at 5:47 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:

> 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
>>>
>>
>>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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