Dear all,
After doing iBI for non-bonded parameters (6 nonbonded interactions) of a
molecule with 4 beads (3 bead types), I am trying to do iBI for both
nonbonded and bonded interactions all together. Although I have paid enough
attention on most of the details in preparing the input files, like
clipping of poorly sampled regions, extrapolation them to out of the region
of interest ... , the bonded(bond-and angle).dist.new are getting worse and
worse in each step respect to the older steps and respect to the *.dist.tgt
whereas the nonbonded interaction are all fine in good agreement with their
targets. The system has 3 bonds and 2 angles to be parameterized along with
the nonbonded ones. The simulation for each step is 4ns after
pre_simulation and below is part of my setting file. Any comment and idea
on the issue would be highly appreciated.
<bonded>
<name>bond-A-B</name>
<min>0.15</min>
<max>2.0</max>
<step>0.005</step>
<inverse>
<target>bond-A-B.dist.tgt</target>
<do_potential>1 0 0</do_potential>
<post_update>smooth</post_update>
<post_update_options>
<scale>0.1</scale>
</post_update_options>
<post_add>convergence</post_add>
<gromacs>
<table>table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
Regards,
Salman
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