2017-06-08 16:24 GMT-06:00 Christoph Junghans <[email protected]>: > 2017-06-08 15:56 GMT-06:00 M. Chakraborty <[email protected]>: >> 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. I meant exclusion method!
Christoph > > 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 [email protected]. >> To post to this group, send email to [email protected]. >> 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 -- 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
