Dear Christoph,
I made a mistake in settings.xml file. Then, it seems to run but it
takes longer than non bonded IBI.
I set the same conditions with non bonded IBI (1 ns and 1fs timestep) but
iteration and updating seem pretty slower.
I have another question.
How to include two mapping xml files in settings.xml? I set them as follow
but only AB bond and ABA angle have been updated each step. CD bond and CDC
angle look the same as AB bond and ABA angle. Do I need to make single
mapping xml file?
<inverse>
<!-- 300*0.00831451 gromacs units -->
<kBT>2.49435</kBT>
<!-- use gromacs as simulation program -->
<program>gromacs</program>
<!-- gromacs specific options -->
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>10</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.002</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>2.5</table_end>
</gromacs>
* <map>DGA.xml</map> <map>J230.xml</map>*
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>500</iterations_max>
<convergence_check>
<type>default</type>
<limit>0.001</limit>
</convergence_check>
<!-- ibm: inverse biltzmann imc: inverse monte carlo -->
<method>ibi</method>
<!-- write log to this file -->
<log_file>inverse.log</log_file>
<!-- write restart step to this file -->
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
Thank you.
Best regards,
Changwoon Jang
On Mon, Feb 1, 2016 at 12:59 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-02-01 10:41 GMT-07:00 Chang Woon Jang <[email protected]>:
> > Dear Votca Users,
> >
> > I found the error message coming from. Sorry about the question.
> To help future users, what was the problem and the solution to it?
>
> >
> >
> > Thank you very much.
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> > On Mon, Feb 1, 2016 at 12:08 PM, Chang Woon Jang <
> [email protected]>
> > wrote:
> >>
> >> Dear Votca Users,
> >>
> >> I would like to run bonded IBI for a polymer system. I followed the
> >> hexane bonded IBI tutorial.
> >>
> >> I have four bead types (A, B, C, D). The number of bonded types is four
> as
> >> follow.
> >>
> >> A-B : A and B are bonded
> >> C-D : C and D are bonded
> >> A-B-A : A and B and A are angled
> >> C-D-C : C and D and C are angled
> >>
> >> I created a cg.xml file containing including all information ABbond,
> >> CDbond, ABAangle. and CDCangle.
> >>
> >> In the settings.xml file, I also indicated and matched those information
> >> in cg.xml file for bond and angle.
> >>
> >> <bonded>
> >> <!-- name of the interaction -->
> >> <name>ABbond</name>
> >> <min>0.48</min>
> >> <max>0.59</max>
> >> <step>0.002</step>
> >> <inverse>
> >> <!-- target distribution -->
> >> <target>ABbond.dist.tgt</target>
> >> <gromacs>
> >> <table>table_b1.xvg</table>
> >> </gromacs>
> >> </inverse>
> >> </bonded>
> >> <bonded>
> >> <bonded>
> >> <!-- name of the interaction -->
> >> <name>CDbond</name>
> >> <min>0.30</min>
> >> <max>0.60</max>
> >> <step>0.002</step>
> >> <inverse>
> >> <!-- target distribution -->
> >> <target>CDbond.dist.tgt</target>
> >> <gromacs>
> >> <table>table_b2.xvg</table>
> >> </gromacs>
> >> </inverse>
> >> </bonded>
> >> <bonded>
> >> <!-- name of the interaction -->
> >> <name>ABAangle</name>
> >> <min>1.2</min>
> >> <max>3.1</max>
> >> <step>0.02</step>
> >> <inverse>
> >> <!-- target distribution -->
> >> <target>ABAangle.dist.tgt</target>
> >> <gromacs>
> >> <table>table_a1.xvg</table>
> >> </gromacs>
> >> </inverse>
> >> </bonded>
> >> <bonded>
> >> <!-- name of the interaction -->
> >> <name>CDCangle</name>
> >> <min>0.8</min>
> >> <max>3.1</max>
> >> <step>0.02</step>
> >> <inverse>
> >> <!-- target distribution -->
> >> <target>CDCangle.dist.tgt</target>
> >> <gromacs>
> >> <table>table_a2.xvg</table>
> >> </gromacs>
> >> </inverse>
> >> </bonded>
> >>
> >>
> >> When I just run as csg_inverse --options settings.xml, it just
> terminated.
> >> IBI and bonded_IBI in hexane tutorials are fine with the command
> csg_inverse
> >> --options settings.xml.
> >>
> >> Also, other non bonded IBI for my system is just fine and run smoothly.
> >>
> >> Would you please give me a comment for this?
> >>
> >> Thank you.
> >>
> >> Best regards,
> >> Changwoon Jang,
> >>
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>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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