[gmx-users] coarse grain dynamics

[Jared James Thompson]

There are programs around for reconstruction of full-atomistic representations
from coarse-grained representations, however. I don't know if there are any
available for the GROMACS architecture.




Quoting Nuno Azoia <nazoia at det.uminho.pt>:

> Hi there!
> 
> I never worked with coarse grain simulations, but if you used a coarse
> grain methodology you didn't include all the atoms, so you didn't
> included hydrogens. So now you can not see them, of course. They are not
> there.
> 
> If you need to "know the hydrogen bond interactions" you need to do some
> "all atoms" simulation, not coarse grain.
> 
> Nuno Azoia
> 
> On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:
> > Dear Gromacs Users,
> > 
> > I have done coarse grain simulation for 2 peptides in bilayer for
> > 1000ns, and now i would like to know the hydrogen bond interactions
> > between these two peptides. Please let me know how to do this, i can
> > visualize the trajectory in VMD, but unable to calculate the hydrogen
> > bonding distance and the hydrogen bonds existing..
> > 
> > Thanks
> > 
> > Ram
> 
> -- 
> Nuno Gonçalo Azoia Lopes
>  
> Laboratório de Investigação em Acabamento
> Departamento de Engenharia Têxtil
> Universidade do Minho
> Campus de Azurém
> 4800-058 Guimarães
> Portugal
>  
> Tel: +351 253 510 280 - Ext: 517 289
> Fax: +351 253 510 293
>  
> Mobile: +351 965 382 487
> E-mail: nazoia at det.uminho.pt
> http://nazoia.net
> 
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 


-- 
Jared James Thompson
Department of Medicinal Chemistry and Molecular Pharmacology
Laboratory for Computational Drug Design and Biology
RHPH 504C
Heine Pharmacy Building
575 Stadium Mall Drive
West Lafayette, IN  47907-2091