Hi,<div><br></div><div>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: <a href="http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt">http://md.chem.rug.nl/cgmartini/index.php/tools/113-rt</a></div>
<div><br></div><div>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.</div>
<div><br></div><div><br></div><div>Esteban G. Vega-Hissi</div><div>UNSL</div><div>San Luis</div><div>Argentina</div><div><br></div><div>--<br><div class="gmail_quote">On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson <span dir="ltr"><<a href="mailto:thompsjj@purdue.edu">thompsjj@purdue.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">There are programs around for reconstruction of full-atomistic representations<br>
from coarse-grained representations, however. I don't know if there are any<br>
available for the GROMACS architecture.<br>
<div><div></div><div class="h5"><br>
<br>
<br>
<br>
Quoting Nuno Azoia <<a href="mailto:nazoia@det.uminho.pt">nazoia@det.uminho.pt</a>>:<br>
<br>
> Hi there!<br>
><br>
> I never worked with coarse grain simulations, but if you used a coarse<br>
> grain methodology you didn't include all the atoms, so you didn't<br>
> included hydrogens. So now you can not see them, of course. They are not<br>
> there.<br>
><br>
> If you need to "know the hydrogen bond interactions" you need to do some<br>
> "all atoms" simulation, not coarse grain.<br>
><br>
> Nuno Azoia<br>
><br>
> On Tue, 2010-05-25 at 16:03 +0200, ram bio wrote:<br>
> > Dear Gromacs Users,<br>
> ><br>
> > I have done coarse grain simulation for 2 peptides in bilayer for<br>
> > 1000ns, and now i would like to know the hydrogen bond interactions<br>
> > between these two peptides. Please let me know how to do this, i can<br>
> > visualize the trajectory in VMD, but unable to calculate the hydrogen<br>
> > bonding distance and the hydrogen bonds existing..<br>
> ><br>
> > Thanks<br>
> ><br>
> > Ram<br>
><br>
> --<br>
> Nuno Gonçalo Azoia Lopes<br>
><br>
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> Universidade do Minho<br>
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><br>
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><br>
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><br>
> --<br>
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<br>
<br>
</div></div><font color="#888888">--<br>
Jared James Thompson<br>
Department of Medicinal Chemistry and Molecular Pharmacology<br>
Laboratory for Computational Drug Design and Biology<br>
RHPH 504C<br>
Heine Pharmacy Building<br>
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West Lafayette, IN 47907-2091<br>
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</div></div></blockquote></div><br></div>