From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Dec 12 2020 - 09:17:32 CST
Hi Asshish, you didn't say which type of variable (function) you used.
Assuming that you used a "distance" function:
https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:cvc_distance
you are defining indeed the distance between the two COMs.
Specifically, the "program" that computes the COMs of groups is actually
NAMD, while Colvars uses them to define the collective variable and the
biasing forces on it that allow you enhanced sampling and PMF computation.
(Instead, other types of collective variables that are not based on COMs
are computed entirely within Colvars.)
In your publication, you should therefore cite both the NAMD and Colvars
papers:
https://doi.org/10.1063/5.0014475
https://doi.org/10.1080/00268976.2013.813594
Thanks,
Giacomo
On Sat, Dec 12, 2020 at 3:18 AM Aashish Bhatt <aashish.ph16221_at_inst.ac.in>
wrote:
> Dear Sir
>
> I have a system with cyclodextrin and peptide. I want to study the
> formation of the inclusion complex via the adaptive biasing force method.
> As discussed in the following paper.
> DOI: 10.1039/c7cp02292a
> I took the group 1 colvar glycosidic bond oxygen atoms and in another
> group 2 selection of heavy atoms of the N terminal or C-terminal amino acid
> residue.
> I want to know whether the program automatically calculates the COM or I
> have to give a different format.
>
>
> Best regards
>
> Aashish
>
>
>
>
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