Re: Restraint on XY Plane

From: Peixi Zhu (tulanezhu_at_gmail.com)
Date: Fri Oct 15 2010 - 00:33:38 CDT

Below is my colvars input file using Umbrella sampling. I'm trying to
obtain PMF at z direction by changing the "centers" variable and run
different simulations. I want to add constraint of my molecule at XY
plain. From the other thread, it seems that I can do it either by setting
the constraints variables in the configuration file, or by making use of the
distanceXY variables in colvars file. Anyone has an idea which is ideal?
For the latter, how to I modify my colvars file? Many thanks.

#begin my colvars input
Colvarstrajfrequency 100
Colvarsrestartfrequency 50

colvar {
   name ProjectionZ

   distanceZ {
      ref {
         dummyAtom ( 21.657, 24.506, 46.027 )
      }
      main {
         atomNumbersRange { 21966-21996 }
      }
   }
}

harmonic {
  colvars ProjectionZ
  centers 24
  forceConstant 5.0
}

#end of colvars input

--Peixi

On Thu, Oct 14, 2010 at 4:12 PM, Peixi Zhu <tulanezhu_at_gmail.com> wrote:

> Hi,
>
> I found from the following thread about creating a cylindrical constraint
> for ABF simulation by using distanceZ and distanceXY variables:
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/11881.html
>
>
> Can someone give out an example of the colvars input file? And if I use
> umbrella sampling rather than ABF to calculate PMF(z), can I constraint
> atoms in a similar way?
>
>
> Thanks a lot,
>
> --Peixi
>

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