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