From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 03 2017 - 12:53:19 CDT
You could try the wrapAround option to define the interval most convenient
to you :-)
http://colvars.github.io/colvars-refman-namd/colvars-
refman-namd.html#x1-510005.3.1
On Thu, Aug 3, 2017 at 11:48 AM, Albers, Thomas <TALBERS_at_augusta.edu> wrote:
> Hello!
>
>
> I would like to explore the energy profile of the conformational change in
> a turn in my protein. The Ramachandran angle phi varies from 50 to 260
> degrees in that system; the range between -100 and 50 degrees is not
> visited.
>
>
> The interval for dihedral angles in NAMD is -180 - 180 degrees. How to get
> around the periodicity issue, because as far as I can see the interval
> beyond 180 deg, where the angle wraps around, is not reached. Here is an
> excerpt from the .count file:
>
>
> ...
>
> 172.5 15805
> 177.5 13467
> 182.5 0
> 187.5 0
> ..
>
> The colvar is defined like this:
>
>
> colvar {
> name phi265
>
> width 5.0
> lowerboundary 50
> upperboundary 260
> lowerWallConstant 0.2
> upperWallConstant 0.2
>
> dihedral {
> group1 { atomNumbers 4365 }
> group2 { atomNumbers 4367 }
> group3 { atomNumbers 4369 }
> group4 { atomNumbers 4372 }
> }
> }
>
> abf {
> colvars phi265
> }
>
> How to get around the wraparound issue?
>
> Thanks,
> Thomas
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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