Hello,
I got back to the files, so was trying to get IBI for bonded, but I
dont understand how should my settings.xml look like and where should
I be supplying "a reasonable potential input ($name.pot.in)" to see
if the module does work.
I will also email Victor the files I had problems with (had no access
for a week to them, very sorry haven't emailed earlier).
This is my current settings file, but I cannot run with it. I guess I
am missing something?
<cg>
<bonded>
<name>E-C</name>
<min>0</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<target>bonds-EC.tgt</target>
<do_potential>1 0 </do_potential>
<post_update>scale</post_update>
<post_update_options>
<scale>1</scale>
</post_update_options>
<post_add></post_add>
<gromacs>
<table>table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
<name>C-C</name>sun it.
<min>0</min>
<max>1.50</max>
<step>0.01</step>
<inverse>
<target>bonds-CC.tgt</target>
<do_potential>0 1 </do_potential>
<post_update>scale</post_update>
<post_update_options>
<scale>1</scale>
</post_update_options>
<post_add></post_add>
<gromacs>
<table>table_b2.xvg</table>
</gromacs>
</inverse>
</bonded>
<!-- general options for inverse script -->
<inverse>
<!-- 250K*0.00831451 gromacs units -->
<kBT>2.0786275</kBT>
<program>gromacs</program>
<gromacs>
<!-- trash so many frames at the beginning -->
<equi_time>10</equi_time>
<!-- grid for table*.xvg !-->
<table_bins>0.002</table_bins>
<!-- cut the potential at this value (gromacs bug) -->
<pot_max>1000000</pot_max>
<!-- extend the tables to this value -->
<table_end>2.0</table_end>
<!-- topology + trajectory. Be careful, do not change yet! -->
<topol>topol.tpr</topol>
<traj>traj.xtc</traj>
<temp_check>no</temp_check>
</gromacs>
<!-- these files are copied for each new run -->
<filelist>grompp.mdp topol.top table.xvg table_a1.xvg table_b1.xvg
table_b2.xvg index.ndx</filelist>
<!-- do so many iterations -->
<iterations_max>100</iterations_max>
<method>ibi</method>
<scriptdir>$PWD</scriptdir>
<log_file>inverse.log</log_file>
<restart_file>restart_points.log</restart_file>
</inverse>
</cg>
Thank you very much,
V
On Oct 3, 11:06 am, Victor Ruehle <[email protected]> wrote:
> Dear Valentina,
>
> thanks for pointing it out. I tested the mapping and bonding stuff for
> quite a few things, never had an issue. My guess is that it is somehow
> connected with the mapping.
>
> Could you please send me some example input where the problem occurs
> directly to [email protected].
>
> Thanks in advance,
> Victor
>
> 2011/10/2 Valentina <[email protected]>:
>
> >> It could be possible that the code in the bonded branch already works
> >> if one provides a reasonable potential input ($name.pot.in) and
> >> ensures the refinement region (min to max) is always well sampled.
>
> > I will try. Thank you.
>
> >> Sounds strange to me, but maybe Victor has an idea. Maybe you can
> >> provide us with a simple case that fails.
>
> > I will put the details as soon as I get to the office (a bit later
> > today).
>
> > Thank you very much,
> > V
>
> > On Oct 2, 1:28 pm, Christoph Junghans <[email protected]> wrote:
> >> Am 2. Oktober 2011 12:02 schrieb Valentina
> >> <[email protected]>:> A, that makes sense. I have done simple
> >> inversion, but its looking
> >> > like i may need a few iterations still.
>
> >> > Also, btw, though I should tell you. I have noticed a bit of a problem
> >> > with bonded potentials produced by csg_botzmann. I have a simple
> >> > molecule that is put into End-Ceter-Center-End bids. I have used
> >> > csg_boltzmann to do inversion and also did it by hand myself to
> >> > compare. Center-Center bonds are perfect, but End-Center ones are not
> >> > right. I haven't yet figured out why.
>
> >> Cheers,
>
> >> Christoph
>
> >> > V
>
> >> > On Oct 2, 8:07 am, Christoph Junghans <[email protected]> wrote:
> >> >> To make it short, IBI for bonded interactions is not implemented yet.
> >> >> It has been on the todo list for a year (issue 11 -
> >> >> <https://code.google.com/p/votca/issues/detail?id=11>) I have started
> >> >> working on this a while ago in the 'bonded' branch of csg, but it is
> >> >> far from being finished.
>
> >> >> However for most systems simple Boltzmann inversion (BI) is enough as
> >> >> bonded interactions are much stiffer.
>
> >> >> Cheers,
>
> >> >> Christoph
>
> >> >> Am 2. Oktober 2011 00:27 schrieb Valentina
> >> >> <[email protected]>:
>
> >> >> > Also, have a error:
> >> >> > # Result of 'csg_property --file /home/d47fvj/C12-BND/settings-BND.xml
> >> >> > --path cg.non-bonded.name --short --print .' was empty #
>
> >> >> > Do I have to have cg.non-bonded. section in any case?
>
> >> >> > Thank you,
> >> >> > V
>
> >> >> > On Oct 1, 11:15 pm, Valentina <[email protected]> wrote:
> >> >> >> Hello,
>
> >> >> >> I am a bit stuck here.
>
> >> >> >> If I want to do IBI for bonded interactions, I will create a CG
> >> >> >> starting .gro and .top
> >> >> >> for .top I would need to feed in a tabulated potential (created by
> >> >> >> initial inversion of distibutions) in the form of table_b1.xvg
>
> >> >> >> so in the settings.xml I provide a target potential bonds-EC.tgt
> >> >> >> <bonded>
> >> >> >> <name>E-C</name>
> >> >> >> <min>0</min>
> >> >> >> <max>1.50</max>
> >> >> >> <step>0.01</step>
> >> >> >> <inverse>
> >> >> >> <target>bonds-EC.tgt</target>
> >> >> >> <do_potential>1 0 0</do_potential>
> >> >> >> <post_update>scale</post_update>
> >> >> >> <post_update_options>
> >> >> >> <scale>1</scale>
> >> >> >> </post_update_options>
> >> >> >> <gromacs>
> >> >> >> <table>table_b1.xvg</table>
> >> >> >> </gromacs>
> >> >> >> </inverse>
> >> >> >> </bonded>
>
> >> >> >> also I have files to be transferred, where I have table_b1.xvg being
> >> >> >> carried through to every new step
> >> >> >> <filelist>grompp.mdp topol.top table.xvg table_a1.xvg
> >> >> >> table_b1.xvg
> >> >> >> table_b2.xvg index.ndx</filelist>
>
> >> >> >> So this is where I am confused, how do I make it to update
> >> >> >> table_b1.xvg after every step?
>
> >> >> >> Many thanks,
> >> >> >> V
>
> >> >> > --
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>
> >> >> --
> >> >> Christoph Junghans
> >> >> Votca Core Developer
>
> >> >> Web:http://www.votca.org
>
> >> > --
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> >> --
> >> Christoph Junghans
> >> Votca Core Developer
>
> >> Web:http://www.votca.org
>
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>
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