Dear Christoph,
After I included the simple pressure correction, it gives me an error
without inverse.log file. It just terminated. Without pressure correction,
IBI runs as usual. Would you give any trouble shooting advice?
running csg_inverse --options "settings.xml"
./run.sh: line 4: 28777 Terminated csg_inverse --options
settings.xml
This is the part of settings.xml. The following reds are what I added.
<!-- example for a non-bonded interaction entry -->
<non-bonded>
<!-- name of the interaction -->
<name>A-A</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>A</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0.32</min>
<max>1.47</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>CG-CG.A-A.dist.tgt</target>
* <p_target>1.0</p_target>*
<!-- update cycles -->
<do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential>
<!-- additional post processing of dU before added to potential -->
* <post_update>pressure</post_update>*
* <post_update_options> <pressure>
<type>simple</type> <do>0 1 1 1 1 1 1 1 1 1 1 1 1 1
1</do> <simple> <scale>0.0003</scale>
</simple> </pressure> </post_update_options>*
<!-- additional post processing of U after dU added to potential -->
<post_add>convergence</post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_A_A.xvg</table>
</gromacs>
</inverse>
</non-bonded>
Thank you.
Best regards,
Changwoon Jang
On Mon, May 16, 2016 at 5:34 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-05-16 15:27 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > Thank you for the quick reply. In the spce/ibi_pressure example,
> > <do_potential> is every second step (ex., 0 1 0) and <do> inside
> <pressure>
> > is every first and third step (1 0 1).
> >
> >
> > Do these <do_potential> and <do> alternatively need to be set? or Can I
> set
> > as I wish as follows?
> You can set them as you wish! In the example we used them alternating.
>
> Christoph
> >
> >
> >
> >
> >
> > Thank you. <non-bonded>
> > <!-- name of the interaction -->
> > <name>A-A</name>
> > <!-- types involved in this interaction -->
> > <type1>A</type1>
> > <type2>A</type2>
> > <!-- dimension + grid spacing of tables for calculations -->
> > <min>0.32</min>
> > <max>1.47</max>
> > <step>0.01</step>
> > <inverse>
> > <!-- target distribution (rdf), just give gromas rdf.xvg -->
> > <target>CG-CG.A-A.dist.tgt</target>
> > <p_target>1.0</p_target>
> > <!-- update cycles -->
> > <do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential>
> > <!-- additional post processing of dU before added to potential -->
> > <post_update>pressure</post_update>
> > <post_update_options>
> > <pressure>
> > <type>simple</type>
> > <do>1 0 1</do>
> > <simple>
> > <scale>0.0003</scale>
> > </simple>
> > </pressure>
> > </post_update_options>
> > <!-- additional post processing of U after dU added to potential
> -->
> > <post_add>convergence</post_add>
> > <!-- name of the table for gromacs run -->
> > <gromacs>
> > <table>table_A_A.xvg</table>
> > </gromacs>
> > </inverse>
> > </non-bonded>
> >
> >
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> >
> >
> > On Mon, May 16, 2016 at 5:05 PM, Christoph Junghans <[email protected]>
> > wrote:
> >>
> >> 2016-05-16 15:00 GMT-06:00 Chang Woon Jang <[email protected]>:
> >> > Dear VOTCA users,
> >> >
> >> >
> >> > I need a help to use pressure correction during nonbond IBI
> >> > calculation. Without the pressure correction, the derived CG
> potentials
> >> > do
> >> > not give the right density close to experiment. The density is much
> >> > lower
> >> > than the experiment. Therefore, I would like to re-derive nonbond
> >> > potentials
> >> > using pressure correction. The previous setting.xml for nonbond IBI is
> >> > like
> >> > below for example. Where do I need to put the <p_target>,
> <post_update>,
> >> > <pressure>, <type>, etc? Do I need to put those blocks in the
> <inverse>
> >> > block?
> >> >
> >> > I am not sure the syntax for the pressure correction. Would you please
> >> > give
> >> > me a comment or example script? Thank you very much.
> >> See the spce/ibi_pressure tutorial:
> >> https://github.com/votca/csg-tutorials/tree/master/spce/ibi_pressure
> >>
> >> The p_target goes into the inverse block and the pressure block under
> >> the post_update_options option.
> >>
> >> Christoph
> >> >
> >> > <non-bonded>
> >> > <!-- name of the interaction -->
> >> > <name>A-A</name>
> >> > <!-- types involved in this interaction -->
> >> > <type1>A</type1>
> >> > <type2>A</type2>
> >> > <!-- dimension + grid spacing of tables for calculations -->
> >> > <min>0.32</min>
> >> > <max>1.47</max>
> >> > <step>0.01</step>
> >> > <inverse>
> >> > <!-- target distribution (rdf), just give gromas rdf.xvg -->
> >> > <target>CG-CG.A-A.dist.tgt</target>
> >> > <!-- update cycles -->
> >> > <do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential>
> >> > <!-- additional post processing of dU before added to potential
> >> > -->
> >> > <post_update></post_update>
> >> > <!-- additional post processing of U after dU added to potential
> >> > -->
> >> > <post_add>convergence</post_add>
> >> > <!-- name of the table for gromacs run -->
> >> > <gromacs>
> >> > <table>table_A_A.xvg</table>
> >> > </gromacs>
> >> > </inverse>
> >> > </non-bonded>
> >> >
> >> >
> >> > Best regards,
> >> > Changwoon Jang,
> >> >
> >> > --
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> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
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> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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