RE: [gmx-users] Dihedral potentials
Hi, In the dihedraltypes section (or any types section), redefining parameters for the same atom types generates a warning (saying it will use the last) and halts grompp, unless you use the -maxwarn option. For CHARMM there will be an exception to this rule in the next release. But I guess you don't mean defining parameters, but interactions in the [ dihedrals ] section. Any interactions listed there are added. If you add an interaction twice, you get double the potential (without warning). Berk From: domm...@icp.uni-stuttgart.de Date: Fri, 16 Apr 2010 12:20:11 +0200 To: gmx-users@gromacs.org Subject: [gmx-users] Dihedral potentials Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Cheers, Flo --Florian DommertDipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert _ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop-- gmx-users mailing listgmx-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
Re: [gmx-users] Dihedral potentials
On Apr 16, 2010, at 3:22 PM, Florian Dommert wrote: Hello Xavier, thank you very much for the quick reply. As I use it in the topol.top file everything is fine, so the dihedrals should add up. yes, I noticed you actually mention it in your email :)) Cheers, Flo On 16.04.2010, at 15:05, XAvier Periole wrote: On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote: Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Depends if you define it in the topology file or in the parameter file. In the topology file the sum would be used. In the parameter file I would think only one would be used ... no idea which but you could check this for a simple system and looking at the tpr file using gmxdump. XAvier Cheers, Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
Re: [gmx-users] Dihedral potentials
Hello Xavier, thank you very much for the quick reply. As I use it in the topol.top file everything is fine, so the dihedrals should add up. Cheers, Flo On 16.04.2010, at 15:05, XAvier Periole wrote: > > On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote: > >> Hello, >> >> I have a question regarding the dihedral section in a topology file. If I >> define two parameters sets for the same dihedral, are the energies added up >> or is the first one replaced by the second one ? Unfortunately there is no >> sentence in the manual regarding this. > Depends if you define it in the topology file or in the parameter file. > In the topology file the sum would be used. > In the parameter file I would think only one would be used ... no idea > which but you could check this for a simple system and looking at > the tpr file using gmxdump. > > XAvier >> >> Cheers, >> >> Flo >> >> >> -- >> Florian Dommert >> Dipl.-Phys. >> >> Institute for Computational Physics >> >> University Stuttgart >> >> Pfaffenwaldring 27 >> 70569 Stuttgart >> >> Phone: +49(0)711/685-6-3613 >> Fax: +49-(0)711/685-6-3658 >> >> EMail: domm...@icp.uni-stuttgart.de >> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert >> >> -- >> gmx-users mailing listgmx-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 > > -- > gmx-users mailing listgmx-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 -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert PGP.sig Description: This is a digitally signed message part -- gmx-users mailing listgmx-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
Re: [gmx-users] Dihedral potentials
On Apr 16, 2010, at 12:20 PM, Florian Dommert wrote: Hello, I have a question regarding the dihedral section in a topology file. If I define two parameters sets for the same dihedral, are the energies added up or is the first one replaced by the second one ? Unfortunately there is no sentence in the manual regarding this. Depends if you define it in the topology file or in the parameter file. In the topology file the sum would be used. In the parameter file I would think only one would be used ... no idea which but you could check this for a simple system and looking at the tpr file using gmxdump. XAvier Cheers, Flo -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -- gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
