Hi, 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 UNSL San Luis Argentina -- On Tue, May 25, 2010 at 4:57 PM, Jared James Thompson <thomp...@purdue.edu>wrote: > 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 <naz...@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: naz...@det.uminho.pt > > http://nazoia.net > > > > -- > > gmx-users mailing list gmx-users@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-requ...@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 > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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