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?
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,
> >
> > --
> > You received this message because you are subscribed to the Google Groups
> > "votca" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to [email protected].
> > To post to this group, send email to [email protected].
> > Visit this group at https://groups.google.com/group/votca.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [email protected].
> To post to this group, send email to [email protected].
> Visit this group at https://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/d/optout.
>
--
You received this message because you are subscribed to the Google Groups
"votca" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.
