Thanks! I had just added that and was going to do a pull request but you beat me to it.
That works much better now with that option. I was still having an issue though with the extrapolation, so I changed the bond, angle and torsion extrapolation to the sasha function in potential_extrapolate.sh. and I'm having a lot less issues now. Is it possible to control this option for the extrapolation option from within the xml? It looked like I could only change it within potential_extrapolate.sh. Thanks. Josh On Friday, March 10, 2017 at 12:43:01 PM UTC-5, Christoph Junghans wrote: > 2017-03-10 0:05 GMT-07:00 Joshua Moore <[email protected] <javascript:>>: > > I am having issues with the bond potential table written during ibi. If > I > > cut it only in the region that should be fit (where the distribution is > > nonzero), it does not extend far enough for LAMMPS, but if I extend this > > region in the bonded section, the extrapolation is not steep enough. > Please > > see the attachment. LAMMPS recently changed so if a bond length is > outside > > the table it gives an error. Previously it would just use the force at > the > > end points. > > > > Is there an option to set only a specific range, but then extend this > when > > writing the table? > > > > Do we need to set the upper and lower end points like the angle > potential in > > potential_to_lammps.sh? It looks like there is an option for Gromacs > but > > not LAMMPS? > Apparently, there was only a <table_begin> option for lammps, but no > <table_end> option (like gromacs has), so I added that: > < > https://github.com/votca/csg/commit/c228c63844efe8789cd0242f1f592b0519c3e701> > > > Christoph > > > > <bonded> > > <!-- name of the interaction --> > > <name>A_A_bond</name> > > <min>2.0</min> > > <max>8.0</max> > > <step>0.01</step> > > <inverse> > > <!-- target distribution --> > > <target>A_A_bond.dist.tgt</target> > > <do_potential>0</do_potential> > > <lammps> > > <table>table_b1.pot</table> > > </lammps> > > </inverse> > > </bonded> > > > > Thanks. > > > > Josh > > > > -- > > 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 > -- 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.
