[gmx-users] coarse grain dynamics

Nuno Azoia nazoia at det.uminho.pt
Tue May 25 16:35:16 CEST 2010

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

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
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

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