2017-06-08 15:56 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Hello, > > I was following the hexane hybrid tutorial and there [exclusions] were > included in the topology file to consider only non-bonded forces for > subsequent force-matching. I a bit confused about how exclusions work since > in the GROMACS manual (Chap. 5 Topologies) it is said that the [exclusions] > section will exclude all the non-bonded interactions between the atom > indices listed. It sounded like the opposite of what was intended in the > hybrid hexane. I am clearly missing something. I would appreciate if someone > can help me to understand it. Thanks. I guess you are referring to the "fmatch_intramolecular" folder, right? The exclusions in that topology are made, to then rerun gromacs on the trajectory without the exclusions. So basically you end up with forces, which have no contributions from the bonds, but are calculated on positions generated by the full interactions set. See the "Model System and Simulation Details" of <http://dx.doi.org/10.1002/mats.201100011> for how the subtraction method works.
Christoph > > M. Chakraborty > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
