Dear all, But I have questions about the energies calculated by GMX for bonds and angles scanning.
For example, a series of conformations of one system should be generated for a bond scanning, the only difference in geometry of these conformations is the bond length A---B. However, when I set the force constant as 0 for bond A---B, the bond energies is not a flat line as the bond length changes, in principle, it should be a flat line, but it is not. <http://gromacs.5086.x6.nabble.com/file/n5010274/bond_1FF.png> This is an example I got for my system. Could some tell me how to explain the energy differences? Thanks very much! All the best, qh -- View this message in context: http://gromacs.5086.x6.nabble.com/Energies-in-MM-scanning-using-gmx-tp5010274.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
