VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Nov 19 2010 - 15:08:10 CST

Branko:

About your question 3: the default behavior for mesure rgyr in VMD
seems to be non-weighted, so it should be the same value as the one
from colvars, except, as Axel said, if periodic boundary conditions
make a difference.

Cheers,
Jerome

On 19 November 2010 20:35, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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 “atomNumbers”), 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
>>         “index”)  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.
>
>