[CP2K:2679] Re: Bond rotation restraint

Ilya ikupc... at gmail.com
Wed Apr 21 15:23:13 UTC 2010


>can you please post the URL of the input reference page where you found

http://cp2k.berlios.de/manual/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/BOND_ROTATION.html

How to set a restraint for the rotation of a bond, e.g. atom12-atom13,
in respect to the line, which is parallel to some axis, e.g. [0,0,1]?

Does it look like this:
   ...
   &SUBSYS
   ...
     &COLVAR
         &BOND_ROTATION
           &POINT
              ATOMS 12
              TYPE GEO_CENTER
           &END POINT
           &POINT
              ATOMS 13
              TYPE GEO_CENTER
           &END POINT
           &POINT
              XYZ 0.0 0.0 0.0
              TYPE FIX_POINT
           &END POINT
           &POINT
              XYZ 0.0 0.0 1.0
              TYPE FIX_POINT
           &END POINT
           P1_BOND1 1
           P2_BOND1 2
           P1_BOND2 3
           P2_BOND2 4
         &END BOND_ROTATION
     &END COLVAR
   &END SUBSYS

?

Sincerely,
Ilya


On 21 апр, 18:00, Ilya <ikupc... at gmail.com> wrote:
> Sorry, I have not noticed your messages, since I was "encrypting" my
> own one.
>
> Thanks a lot for an instant reply.
> I beg your pardon for my English.
> I am working on it.
>
> Sincerely,
> Ilya
>
> On 21 апр, 17:53, Ilya <ikupc... at gmail.com> wrote:
>
>
>
> > Please, help me.
>
> > I send a sample file if needed.
>
> > And, could someone explain what are the values used in "(X-X0)" in
> > case of an angle(rotational?) restraint? Angle values or cos/sin?
> > An if values are implied what are the units - degrees, radians, pi?
>
> > Sincerely,
> > Ilya
>
> > On 21 апр, 16:04, Ilya <ikupc... at gmail.com> wrote:
>
> > > If use 2 bonds restraint, the bonds are in different parts of system
> > > and not connected i.e. I can not apply common angle or torsional
> > > restraints.
>
> > > On 21 апр, 16:00, Ilya <ikupc... at gmail.com> wrote:
>
> > > > Hello.
>
> > > > I would like to set a restraint for the angle between two bonds, or
> > > > better between a bond and Z axis.
>
> > > > I use the following keys:
>
> > > >    &SUBSYS
> > > >     ...
> > > >    &COLVAR
> > > >        &BOND_ROTATION
> > > >             P1_BOND1 86 #these are atom indexes
> > > >             P1_BOND2 12
> > > >             P2_BOND1 85
> > > >             P2_BOND2 13
> > > >       &END BOND_ROTATION
> > > >      &END COLVAR
> > > >    &END SUBSYS
> > > >    ...
> > > >    &CONSTRAINT
> > > >      &COLLECTIVE
> > > >        TARGET   0.0
> > > >        MOLNAME q1010c-dyn
> > > >        COLVAR 1
> > > >        &RESTRAINT
> > > >           k [kjmol] 1.0
> > > >        &END RESTRAINT
> > > >      &END COLLECTIVE
> > > >    &END CONSTRAINT
>
> > > > But I can not see any effect during my MD.
> > > > I have single molecule in system called "q1010c-dyn"
>
> > > > Could anyone tell me, should I just increase restraint k value, or
> > > > change input, or allot 2 molecules instead of 1, or whatever?
> > > > Just how it should work?
>
> > > > Thanks.
> > > > Ilya
>
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