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?
<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
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