Dear Erik, Many thanks for your comment.
The situation seems to be similar to TIP4P water model where the M site is located among the three other atoms. In my case, it's between the two C-H atoms. Could I ask you which parameters must be selected for these virtual sites? The interest molecule is n-alkane that have (2n+2) C-H bond. Is that make sense that I put the virtual sites there? Best Rasoul On Mon, Feb 11, 2013 at 5:33 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Try virtual sites constructions. > > > On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: > >> Dear All, >> >> I need to define interaction sites on the center of C-H bonds instead >> of nuclei of each atom. The main reason was that non-bonding >> parameters (sigma and epsilon) have been parametrized in these centers >> and those are only available for the center of C-H. >> >> >> So, I just wanted to know how calculation of force can be implemented >> by GROMACS in this case. >> >> >> >> Best wishes >> Rasoul >> -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > 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/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists