2017-03-10 0:05 GMT-07:00 Joshua Moore <[email protected]>: > 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]. > 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.
