2017-03-10 12:01 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: > 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. Does this work for you: <https://github.com/votca/csg/pull/203> ? > > 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 <jdm...@ncsu.edu>: >> > 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 votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@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.
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