Re: Restraint on XY Plane

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Fri Oct 15 2010 - 10:39:24 CDT

Hello Peixi, you got almost the whole thing written down. To define the
distanceXY, you just need to copy over the block for the projectionZ colvar,
and replace "Z" with, "XY" ;-)

Giacomo

---- ----
  Dr. Giacomo Fiorin
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

On Fri, Oct 15, 2010 at 1:33 AM, Peixi Zhu <tulanezhu_at_gmail.com> wrote:

> 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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