# Re: COLVARs for Cremer-Pople puckering parameters in NAMD Metadynamics

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Oct 07 2020 - 05:26:59 CDT

Hi Chythra,

the original Cremer-Pople puckering parameters are not part of the standard set of variables. However, there is an alternate definition as linear combinations of torsion (dihedral) angles:
[ https://pubs.acs.org/doi/10.1021/ct401013s | https://pubs.acs.org/doi/10.1021/ct401013s ]

That is easy to define in the Colvars module ( [ https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvars_crash_course | Crash Course section of the Colvars Module documentation ] ).

The input for these coordinates Zx and Zy would look like this (adding in the correct atom numbers):

colvar {
name Zx
dihedral {
componentCoeff -0.40450849718 # 1.0 / 2 * cos(4 pi / 5)
group1 { atomNumbers x } # Enter atoms for angle nu_1
group2 { atomNumbers x }
group3 { atomNumbers x }
group4 { atomNumbers x }
}
dihedral {
componentCoeff -0.40450849718
group1 { atomNumbers x } # Enter atoms for angle nu_3
group2 { atomNumbers x }
group3 { atomNumbers x }
group4 { atomNumbers x }
}
}
colvar {
name Zy
dihedral {
componentCoeff -0.40450849718 # 1.0 / 2 * cos(4 pi / 5)
group1 { atomNumbers x } # Enter atoms for angle nu_1
group2 { atomNumbers x }
group3 { atomNumbers x }
group4 { atomNumbers x } } dihedral {
componentCoeff 0.40450849718 # -1.0 / 2 * cos(4 pi / 5)
group1 { atomNumbers x } # Enter atoms for angle nu_3
group2 { atomNumbers x }
group3 { atomNumbers x }
group4 { atomNumbers x }
}
}

Please don't forget cite the [ https://www.tandfonline.com/doi/full/10.1080/00268976.2013.813594 | Colvars Module reference paper ] when you use it.

Best,
Jerome

----- On 7 Oct 20, at 4:57, Chythra J N <jn_chythra_at_iitgn.ac.in> wrote:

> Hi,

> I am trying to carry out *Well-Tempered Metadynamics in NAMD for sugars*.
> Is there a *COLVARs module to incorporate Cremer-Pople puckering
> parameters*(Phi,
> theta) similar to dihedrals? If not, kindly advise me if it is possible to
> merge/loop existing COLVARs to obtain the desired function in colvarsConfig
> file.