VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 17 2012 - 10:24:19 CDT

Hi,
  You didn't say anything about whether these individual chains are
tagged in some way in the structure files (e.g. with different chain names,
or some other tag you could use to identify them)? What about the range
of atom indices? If the atoms in each of those changes are in a
strictly consecutive sequence. For convenience you could you could
make atom selection macros that map some easy to type thing like "part1"
to index range selections like "index 739 to 9467".

Cheers,
  John

On Thu, Aug 16, 2012 at 04:04:47PM +0000, simao.pereira_at_di3.units.it wrote:
> Hi all,
>
>
>
> I have a system with a nanoparticle and several chains grafted onto it. I
> would like to do some measurements on each chain (for instance radii of
> gyration).
>
> The issue is that there is no straight way to select each individual chain
> (as far as I know).
>
> Is there a way to select each chain, starting from the atom at the
> grafting point until the end of the chain?
>
> I thought about selecting atoms by their connectivity but since chains are
> long (100 CRU) that may be a bit cumbersome.
>
> Any (good) suggestion is welcome :)
>
>
>
> Best,
>
>
>
> Simao Pereira
>
>
>
> P.S.: I have been using Materials Studio to create the initial system and
> LAMMPS to carry out the dynamics.
>
>
>
> #############################################
>
> PhD Student
>
> DI3 - University of Trieste
>
> Via Valerio 10 - 34127 Trieste (Italy)
>
> Mobile +39 3201860285
>
> Email: simao.pereira_at_di3.units.it
>
> #############################################
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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