VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 19 2010 - 13:35:45 CST

On Fri, 2010-11-19 at 19:44 +0100, Branko wrote:
> Axel,
>
>
>
> I use gyration as colvar (in combination with distance) to obtain 3D
> free energy surface for set of molecules. Gyration – colvar as
> defined in NAMD manual do not include masses of atoms included.
>
> When I analyze trajectory and measure rgyr of atoms defined by colvar
> used, accordance is OK, as far as heavy atoms Br and Cl are not part
> of molecule. Please let me know next:
>
>
>
> 1. Is colvar used in ABF include atomic masses (if atoms are
> described as “atomNumbersâ€), or simply measure radius of gyration of
> atomic positions (providing that every position have a same weight).

you have to ask this the authors of the colvars package.

> 1. How (explicitly) to include mass as weighting factor in script
> that you made previously.

you can (and should) look this up in the VMD user's guide.

> 1. Is “measure rgyr selection†(providing that selection is
> “indexâ€) give output comparable with colvar that I use in ABF
> calculation (see under 1).

again, this is a question to the colvars authors.
the only VMD related aspect here are periodic boundaries.
measure rgyr does not take them into account. you have
to use pbctools to transform/unwrap your trajectory
accordingly, if needed.

axel.

>
>
>
> Thanks
>
>
>
> Branko 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.