2016-01-22 13:15 GMT-07:00 Chang Woon Jang <[email protected]>: > Dear Votca Users, > > I would like to run IBI using csg_inverse. > > I am looking at tutorials at hexane and propane. > > My question is what table_a1.xvg and table_a2.xvg files are. > > Are those initial nonbonded tabulated guess potentials for A and B? Where > do they come from? These are tabulated potential for the bonded interaction, see details on name convention see Sec "4.2.14 Tabulated bonded interaction functions" of the Gromacs manual. In short "a1" is the tabulated angle #1 and "b1" is the tabulated bond #1, where the # showing up in the 4th column of the [bonds] (or 5th column of the [angles]) block in topol.top (the gromacs topology.)
The tables came from Boltzmann inverting the bond and angle distributions. We used csg_boltzmann at the time of the 1st VOTCA paper. Please note that in the hexane/ibi example these interaction are not iterated, but they are fixed. > > If so, can I first obtain those initial guess potentials from STOCK or force > matching method using csg_fmatch? These are fixed and not used as initial guess potentials. And yeah these days you could get them from STOCK and csg_fmatch. In the hexane/ibi_bonded example the bonded interaction are iterated as well. In this example you only have to provide distributions to VOTCA. Christoph > > Thank you very much. > > > Best regards, > Changwoon Jang, > > -- > 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 -- 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.
