# Re: Restraint on XY Plane

From: Peixi Zhu (tulanezhu_at_gmail.com)
Date: Fri Oct 15 2010 - 11:24:26 CDT

Thanks, Giacomo

Does the following script look right:

#begin my colvars input
Colvarstrajfrequency 100
Colvarsrestartfrequency 50

colvar {
name ProjectionZ

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

colvar {
name ProjectionXY

distanceXY {
ref {
dummyAtom ( # Here I will put a different coordinate XYZ # )
}
main {
atomNumbersRange { 21966-21996 }
}
}
}

harmonic {
colvars ProjectionZ ProjectionXY
centers 24
forceConstant 5.0
}

#end of colvars input

I would also like to ask a few more questions:

1. Since I'm only interested in PMF along z coordinate. Will the distanceXY
colvar block by any chance create problem of sampling along z? From what I
understand it shouldn't, but I just want to make sure.

2. Will the distanceXY block hurt computation performance? If the answer is
yes, any idea how much longer it will take for real cluster run time?

3. I read from NAMD manual that the forceConstant divided by sqaure of width
is the real force constant which goes to WHAM. Since I don't have width
defined here, what will my real force constant be?

4. What will my *.colvars.traj output look like? I know that without the
distanceXY block it has only two columns, which are simulation step and
distance. I image that there might be four columns in this case. Then
should I just discard the columns that correspond to distanceXY before I use
WHAM?

Thanks,

--Peixi

On Fri, Oct 15, 2010 at 10:39 AM, Giacomo Fiorin
<giacomo.fiorin_at_temple.edu>wrote:

> 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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