From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Dec 14 2017 - 14:40:22 CST
Hi Ben,
Yes. Define a *single* colvar that has two (or more) components, which
by default get added together. Here is an example from my own research,
were I wanted a colvar (which I call cnumber) to be the difference
between two coordination number colvars.
colvar {
name cnumber
coordNum {
group1 {
atomsFile tagged.pdb
atomsCol B
atomsColValue 1
}
group2 {
atomsFile tagged.pdb
atomsCol B
atomsColValue 2
}
cutoff 8.0
expNumer 4
expDenom 10
componentCoeff 1
}
coordNum {
group1 {
atomsFile tagged.pdb
atomsCol B
atomsColValue 1
}
group2 {
atomsFile tagged.pdb
atomsCol B
atomsColValue 3
}
cutoff 8.0
expNumer 4
expDenom 10
componentCoeff -1
}
}
The componentCoeff is the important part (see
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node57.html#SECTION000134400000000000000).
Then you'd restrain as usual.
-Josh
On 12/14/2017 12:58 PM, Ben Adams wrote:
> Hi,
>
> My question is related to colvar module:
> Is there any way to define a collective variable as a combination of
> other colvars?
> Let's say I have two colvars 'c1' and 'c2' but I want to constrain
> 'c3' at a constant value and c3=a*c1+b*c2.
>
> Regards,
>
> Ben.
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