Thanks. On Thursday, 8 June 2017 18:24:21 UTC-4, Christoph Junghans wrote: > > 2017-06-08 15:56 GMT-06:00 M. Chakraborty <[email protected] > <javascript:>>: > > 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 [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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