Dear Christoph,
Thank you for your reply.
I have another question. After using the scaling value as low as 0.000003
for the pressure correction, there is still lots of fluctuation in pressure
of my system. It does stabilizes for some iterations in the beginning,
though it never reaches even close to the p_target. After initial
stabilization it again fluctuates a lot.
Can you please suggest how to workaround this?
I am hereby attaching my settings.xml file for your reference.
Thank you.
Sanjeet
On Friday, November 11, 2022 at 9:50:15 AM UTC-5 Christoph Junghans wrote:
> On Thu, Nov 10, 2022 at 7:52 PM Sanjeet Singh <[email protected]> wrote:
> >
> > Hello Christoph,
> >
> > Thank you for your support and guidance.
> >
> > Now, IBI is working for me. And I have already started the pressure
> correction step. But, I am not able to stabilize the pressure in my system,
> which is fluctuating a lot. Can you please point out the reason why is it
> so?
> That is very common, I would try to scale down the update from the
> pressure correction.
>
> >
> > I am hereby attaching my settings.xml file, and the lammps.pressure file
> after 50 iterations.
> >
> > I would also like to know that is it ok to perform the potential update
> and pressure correction at the same step of the iteration?
> That depends on the system, but I wouldn't do it at the same time.
>
> >
> > Also, what is the unit of p_target in the settings.xml file?
> It is the same units as whatever your MD program prints out.
>
> Christoph
> >
> > Thank you.
> >
> > Sanjeet
> >
> > On Wednesday, November 9, 2022 at 11:26:33 PM UTC-5 Christoph Junghans
> wrote:
> >>
> >> On Wed, Nov 9, 2022, 20:27 Sanjeet Singh <[email protected]> wrote:
> >>>
> >>> Dear Christoph,
> >>>
> >>> Thank you for your response.
> >>>
> >>> I have some doubt regarding the post_update_options.scale. I have six
> types of non-bonded interaction in my system and I want to update them at
> the same iteration step, then shall I use the scale factor as 1/6 (0.167)
> approximately for each of them?
> >>>
> >>> Similarly, for the post_update_options.pressure.simple.scale, if I
> want to update all of my six interaction at the same step, then what should
> be the value of the scale factor?
> >>>
> >>> I mean if it is related to the compressibility of the system, then if
> my polymer has a compressibility value of 1. Then, what should be the value
> of the scale factor for each of my interaction. Will it be again 1/6?
> >>>
> >>> Or, how to decide upon the weightage I can give to each of the six
> interactions with respect to the scale factor for pressure update?
> >>>
> >>> Can it be related to the fraction of each bead in my system? Or, the
> bead with higher fraction will have higher weightage?
> >>
> >> I could now speculate, but the short answer is, I don't know! All these
> things are very system-specific and you will have figure it out by try and
> error.
> >>
> >> My only advice is too not try too many things at once. Get IBI to work
> then add pressure correction etc.
> >>
> >> Sorry,
> >>
> >> Christoph
> >>
> >>>
> >>> Thank you.
> >>>
> >>> Sanjeet
> >>>
> >>> On Tuesday, November 8, 2022 at 10:04:02 PM UTC-5 Christoph Junghans
> wrote:
> >>>>
> >>>> On Tue, Nov 8, 2022 at 7:23 PM Sanjeet Singh <[email protected]>
> wrote:
> >>>> >
> >>>> > Dear Christoph,
> >>>> >
> >>>> > In the settings.xml file what should be the value of cg. inverse.
> kBT, if am using LAMMPS (real units) as a simulation program as shown below:
> >>>> >
> >>>> > <inverse>
> >>>> > <kBT>2.49435</kBT>
> >>>> > </simulation>
> >>>> > <program>lammps</program>
> >>>> > <!-- lammps specific options -->
> >>>> >
> >>>> > If my T = 300 K, should it be 300 * 0.00198720 = 0.5962 kcal/mol K,
> or 300 * 0.0083144621 = 2.49434 kJ/mol K.
> >>>> You should use 0.5962, but honestly it isn't used in my place besides
> >>>> being the prefactor of the update and you already scaled down the
> >>>> update with a factor 0.1 So it shouldn't matter much.
> >>>>
> >>>> Christoph
> >>>> >
> >>>> > Thank you.
> >>>> >
> >>>> > Sanjeet
> >>>> > On Tuesday, November 8, 2022 at 2:59:36 PM UTC-5 Christoph Junghans
> wrote:
> >>>> >>
> >>>> >> On Tue, Nov 8, 2022 at 12:05 PM Sanjeet Singh <[email protected]>
> wrote:
> >>>> >> >
> >>>> >> > Hello Christoph,
> >>>> >> >
> >>>> >> > I applied all your suggestions and replaced the tabulated bond
> stretching potential with the harmonic functional form. And now I am
> getting somewhat improved result.
> >>>> >> Good, I always recommend doing non-bonded only first and then
> throwing
> >>>> >> the bonded interactions later.
> >>>> >>
> >>>> >> >
> >>>> >> > But, again convergence problem is there. Furthermore, at some
> steps of the iterations, I found that two beads of my system are in direct
> contact with each other.
> >>>> >> >
> >>>> >> > Can you please point out the reason for this, and the possible
> remedy?
> >>>> >> That is a very system specific question. But I guess you will have
> to
> >>>> >> increase the repulsive core of the non-bonded interactions.Check
> the
> >>>> >> file <name>.pot (or whatever name you picked in the settings file)
> in
> >>>> >> the last step_* directory to see if it is extrapolated/repulsive
> >>>> >> enough.
> >>>> >> Usually you can do that by increasing the repulsive core by
> increasing
> >>>> >> the <min> of said interaction a bit.
> >>>> >>
> >>>> >> Christoph
> >>>> >> >
> >>>> >> > I am also attaching snapshots of the simulation box for your
> reference.
> >>>> >> >
> >>>> >> > Thank you.
> >>>> >> >
> >>>> >> > Sanjeet
> >>>> >> >
> >>>> >> > On Monday, November 7, 2022 at 9:34:22 AM UTC-5 Christoph
> Junghans wrote:
> >>>> >> >>
> >>>> >> >> On Sun, Nov 6, 2022 at 6:47 PM Sanjeet Singh <
> [email protected]> wrote:
> >>>> >> >> >
> >>>> >> >> > Hello Christoph,
> >>>> >> >> >
> >>>> >> >> > I am trying to perform IBI for non-bonded interaction. I have
> 3 bead types in my system.
> >>>> >> >> >
> >>>> >> >> > I have already run it for more than 500 iterations, but IBI
> is not able to reproduce the target distribution.
> >>>> >> >> >
> >>>> >> >> > Can you please suggest on how to work on this?
> >>>> >> >> I look like you don't have enough statistics in each iteration,
> you
> >>>> >> >> could do the following:
> >>>> >> >> - more MD steps
> >>>> >> >> - decrease the step size - 0.002 seems a bit too small
> >>>> >> >> - using scale and potential_do will also throw out some of the
> stats.
> >>>> >> >>
> >>>> >> >> Regarding the peak around 0.35nm in the Bead2-Bead2 plot, it
> seems to
> >>>> >> >> me you count an intra-moleculde pair there.
> >>>> >> >> If that is the case, you will need to exclude that.
> >>>> >> >> You can search the mailing for more details, but in short, just
> add a
> >>>> >> >> bond section in your topology.xml (see
> >>>> >> >>
> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/atomistic/hexane.xml#L26
> )
> >>>> >> >> and use said topology file instead of the data file.
> >>>> >> >> Inttra molecular interaction will automatically generate
> exclusion,
> >>>> >> >> you can check that with: csg_dump --top topology.xml --excl
> >>>> >> >>
> >>>> >> >> Christoph
> >>>> >> >>
> >>>> >> >> >
> >>>> >> >> > I am hereby attaching the rdf for two of the non-bonded
> interactions in my system along with the setting.xml file.
> >>>> >> >> >
> >>>> >> >> > Thank you.
> >>>> >> >> >
> >>>> >> >> > Sanjeet
> >>>> >> >> >
> >>>> >> >> >
> >>>> >> >> > --
> >>>> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >>>> >> >> > ---
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> https://groups.google.com/d/msgid/votca/560c96cd-e0f7-4bb7-a339-8e031c1bdab1n%40googlegroups.com
> .
> >>>> >> >>
> >>>> >> >>
> >>>> >> >>
> >>>> >> >> --
> >>>> >> >> Christoph Junghans
> >>>> >> >> Web: http://www.compphys.de
> >>>> >> >
> >>>> >> > --
> >>>> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >>>> >> > ---
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> it, send an email to [email protected].
> >>>> >> > To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/9b5b82f3-b37e-45e1-985d-e505c4bc9d2en%40googlegroups.com
> .
> >>>> >>
> >>>> >>
> >>>> >>
> >>>> >> --
> >>>> >> Christoph Junghans
> >>>> >> Web: http://www.compphys.de
> >>>> >
> >>>> > --
> >>>> > Join us on Slack: https://join.slack.com/t/votca/signup
> >>>> > ---
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> https://groups.google.com/d/msgid/votca/b36d2e4f-8a2b-48a4-8326-2bf69151d04bn%40googlegroups.com
> .
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Christoph Junghans
> >>>> Web: http://www.compphys.de
> >>>
> >>> --
> >>> Join us on Slack: https://join.slack.com/t/votca/signup
> >>> ---
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> an email to [email protected].
> >>>
> >>> To view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/1c62f79e-e530-4d33-9b50-a81cbe95dd34n%40googlegroups.com
> .
> >
> > --
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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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>0.336</min>
<max>0.75</max>
<step>0.002</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</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</do>
<simple>
<scale>0.000003</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>0.03</table_begin>
<table_end>0.755</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>0.3</min>
<max>0.75</max>
<step>0.002</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</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</do>
<simple>
<scale>0.000003</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>0.02</table_begin>
<table_end>0.755</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>0.332</min>
<max>0.75</max>
<step>0.002</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</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</do>
<simple>
<scale>0.000003</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>0.06</table_begin>
<table_end>0.755</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>0.32</min>
<max>0.75</max>
<step>0.002</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</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</do>
<simple>
<scale>0.000003</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>0.04</table_begin>
<table_end>0.755</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>0.31</min>
<max>0.75</max>
<step>0.002</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</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</do>
<simple>
<scale>0.000003</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>0.02</table_begin>
<table_end>0.755</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>0.318</min>
<max>0.75</max>
<step>0.002</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</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</do>
<simple>
<scale>0.000003</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>0.04</table_begin>
<table_end>0.755</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</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 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.log</log_file>
<restart_file>restart.log</restart_file>
</inverse>
</cg>
