thanks, but i am using gromacs version 4.0.07
On Tue, May 25, 2010 at 5:05 PM, Esteban Gabriel Vega Hissi <egv...@gmail.com> wrote: > 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-us...@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-us...@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 > > > -- > gmx-users mailing list gmx-us...@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 > -- 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