[gmx-users] coarse grain dynamics
Esteban Gabriel Vega Hissi
egvega at gmail.com
Tue May 25 17:05:34 CEST 2010
To change between representations (atomistic <--> coarse grained), if you
are using the MARTINI FF, you can use the modified version of Gromacs 3.3,
check here: http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt
If you don't want to switch to full-atomistic representation, check which CG
atom types are able to form hydrogen bonds and look for interactions between
them. Obviously, this will be an approximation.
Esteban G. Vega-Hissi
On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson
<thompsjj at purdue.edu>wrote:
> There are programs around for reconstruction of full-atomistic
> 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
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> > Mobile: +351 965 382 487
> > E-mail: nazoia at det.uminho.pt
> > http://nazoia.net
> > --
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> Jared James Thompson
> Department of Medicinal Chemistry and Molecular Pharmacology
> Laboratory for Computational Drug Design and Biology
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