Hello Christoph,
I am working on a Polymer-Water system and polymer is the bulk entity of my
system.
I am trying to get the CG non-bonded potential for the Polymer-Water system
using IBI. I have 10 different types of interaction in my system. And IBI
is not able to reproduce the RDF for the Water-Water interaction and
Polymer-Water interaction. I mean it is converging to a certain extent
only. And the CG potential I am getting is unstable, especially for the
Water-Water interaction. I am working on this, but not able to figure this
out.
I am hereby attaching the settings.xml file. Bead4 corresponds to water.
Bead1 and Bead3 correspond to the terminal bead of the polymer. Bead2
corresponds to the internal bead of the polymer.
Can you please look into this.
Thank you.
Sanjeet
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<cg>
<!-- FIRST TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead1-Bead1</name>
<!-- types involved in this interaction -->
<type1>Bead1</type1>
<type2>Bead1</type2>
<min>0.35</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead1-Bead1.dist.tgt</target>
<do_potential>1 0 0 0 0 0 0 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 0 0 0 0 0 0 1</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM, SLOPE OF THE PRESSURE CORRECTION -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead1-Bead1.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- SECOND TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead2-Bead2</name>
<type1>Bead2</type1>
<type2>Bead2</type2>
<min>0.35</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead2-Bead2.dist.tgt</target>
<do_potential>0 1 0 0 0 0 0 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 0 0 0 0 0 1 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<!--<post_update>smooth</post_update>-->
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead2-Bead2.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.06</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- THIRD TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead3-Bead3</name>
<type1>Bead3</type1>
<type2>Bead3</type2>
<min>0.35</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead3-Bead3.dist.tgt</target>
<do_potential>0 0 1 0 0 0 0 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 0 0 0 0 1 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead3-Bead3.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- FOURTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead1-Bead2</name>
<type1>Bead1</type1>
<type2>Bead2</type2>
<min>0.35</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead1-Bead2.dist.tgt</target>
<do_potential>0 0 0 1 0 0 0 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 0 0 0 1 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead1-Bead2.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.09</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- FIFTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead2-Bead3</name>
<type1>Bead2</type1>
<type2>Bead3</type2>
<min>0.35</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead2-Bead3.dist.tgt</target>
<do_potential>0 0 0 0 1 0 0 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 0 0 1 0 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM, SLOPE OF THE PRESSURE CORRECTION -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead2-Bead3.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.07</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- SIXTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead1-Bead3</name>
<type1>Bead1</type1>
<type2>Bead3</type2>
<min>0.35</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead1-Bead3.dist.tgt</target>
<do_potential>0 0 0 0 0 1 0 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 0 1 0 0 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead1-Bead3.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.1</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- SEVENTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead1-Bead4</name>
<type1>Bead1</type1>
<type2>Bead4</type2>
<min>0.30</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead1-Bead4.dist.tgt</target>
<do_potential>0 0 0 0 0 0 1 0 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 0 1 0 0 0 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead1-Bead4.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.0005</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- EIGHTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead2-Bead4</name>
<type1>Bead2</type1>
<type2>Bead4</type2>
<min>0.30</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead2-Bead4.dist.tgt</target>
<do_potential>0 0 0 0 0 0 0 1 0 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 0 1 0 0 0 0 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead2-Bead4.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.0006</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- NINTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead3-Bead4</name>
<type1>Bead3</type1>
<type2>Bead4</type2>
<min>0.30</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead3-Bead4.dist.tgt</target>
<do_potential>0 0 0 0 0 0 0 0 1 0</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>0 1 0 0 0 0 0 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead3-Bead4.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.0002</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- TENTH TYPE OF NON-BONDED -->
<non-bonded>
<name>Bead4-Bead4</name>
<type1>Bead4</type1>
<type2>Bead4</type2>
<min>0.29</min>
<max>1.452</max>
<step>0.01</step>
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT>
<p_target>1.0</p_target>
<target>Bead4-Bead4.dist.tgt</target>
<do_potential>0 0 0 0 0 0 0 0 0 1</do_potential> <!-- 1 0 0 WILL UPDATE THE POTENTIAL AT 1st STEP AND WILL NOT UPDATE IN THE SECOND AND 3RD STEP, AND THE CYCLE WILL CONTINUE-->
<post_update>pressure</post_update>
<!--<post_update>pressure</post_update>-->
<post_update_options>
<pressure> <!-- POST UPDATE PRESSURE CORRECTION -->
<type>simple</type>
<do>1 0 0 0 0 0 0 0 0 0</do>
<simple>
<scale>0.00003</scale> <!-- THIS IS RELATED TO THE COMPRESSIBILITY OF THE SYSTEM -->
</simple>
</pressure>
</post_update_options>
<post_update>smooth</post_update>
<post_update_options>
<smooth> <!-- POST UPDATE SMOOTH OPERATIONS OF POTENTIAL UPDATE -->
<iterations>4</iterations> <!-- NUMBER OF TRIANGULAR SMOOTH ITERATIONS TO BE PERFORMED ON POTENTIAL UPDATE-->
</smooth>
<scale>0.1</scale> <!--SCALE FACTOR FOR THE UPDATE-->
</post_update_options>
<post_add>convergence</post_add>
<lammps>
<!-- name of the table for lammps run -->
<table>Bead4-Bead4.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.000001</table_begin>
<table_end>1.452</table_end>
<table_bins>0.005</table_bins>
</lammps>
</inverse>
</non-bonded>
<!-- general options for inverse script -->
<inverse>
<!-- 300*0.0019872036 lammps "real" units kcal/mol -->
<kBT>0.59616108</kBT> <!--THIS IS CORRECT. I HAVE CHECKED FROM SPCE IBI_LAMMPS TUTORIAL-->
<simulation>
<tasks>1</tasks> <!--THIS OPTION IS USED TO GIVE THE NUMBER OF THREADS (-NT) USED TO CALCULATE THE RDF BY USING THE csg_stat COMMAND-->
</simulation>
<!-- use lammps as simulation program -->
<program>lammps</program>
<!-- lammps specific options -->
<lammps>
<command>lmp</command> <!--THIS IS USED TO GIVE THE COMMAND USED TO RUN LAMMPS-->
<opts>-in ${script}</opts> <!--THIS IS USED TO GIVE THE OPTION USED TO RUN LAMMPS-->
<tasks>1</tasks> <!--THIS IS USED TO GIVE THE NUMBER OF THREADS USED TO RUN LAMMPS-->
<pressure_file>lammps.pressure</pressure_file>
<!-- lammps script to run !-->
<script>MY.in</script>
<!-- topology to be used by csg_stat !-->
<topol>topology-CG.xml</topol>
<!-- traj file created by lammps !-->
<traj>traj.dump</traj>
<!--<conf>model.txt</conf> -->
<!--<conf_out>hex.out.data</conf_out>-->
</lammps>
<map>PEO-CG.xml water-CG.xml</map>
<initial_configuration>maindir</initial_configuration>
<!-- these files are copied for each new run -->
<filelist>PEO-CG-TOPOLOGY.data topology-CG.xml PEO-CG.xml water-CG.xml MY.in BOND-AB.pot BOND-BB.pot BOND-BC.pot ANGLE-ABB.pot ANGLE-BBB.pot ANGLE-BBC.pot DIHEDRAL-ABBB.pot DIHEDRAL-BBBB.pot DIHEDRAL-BBBC.pot</filelist>
<!-- do so many iterations -->
<iterations_max>1000</iterations_max>
<convergence_check>
<type>default</type>
<limit>0.05</limit>
</convergence_check>
<!-- ibi: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
<log_file>inverse-0.6-1.log</log_file>
<restart_file>restart.log</restart_file>
</inverse>
</cg>
