I'm trying to calculate the target rdf for polymer system with the
"csg_stat" and also I'm interested to calculate the rdf in the
iterations:
csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg
mapping.xml
I have P3HT system. Every monomer divided on the three beads.
Thiophene ring represented the first bead and hexyl chain divided on
the two beads - each bead include three carbon atoms.
in the settings.xml file I specified the types of the beads which are
the same like in the mapping.xml:
.............
<non-bonded>
<!-- name of the interaction -->
<name>P1-P1</name>
<!-- types involved in this interaction -->
<type1>A</type1>
<type2>A</type2>
<!-- dimension + grid spacing of tables for calculations -->
<min>0</min>
<max>1.36</max>
<step>0.01</step>
<inverse>
<!-- target distribution (rdf), just give gromas rdf.xvg -->
<target>P1-P1.dist.tgt</target>
<!-- update cycles -->
<do_potential>1 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></post_add>
<!-- name of the table for gromacs run -->
<gromacs>
<table>table_P1_P1.xvg</table>
</gromacs>
</inverse>
</non-bonded>
...............
---mapping.xml---:
<cg_molecule>
<name>P3HT</name>
<ident>Protein_X</ident>
<topology>
<cg_beads>
<cg_bead>
<name>S1</name>
<type>A</type>
<symmetry>1</symmetry>
<mapping>A</mapping>
<beads> 1:BBB:S01 1:BBB:C01 1:BBB:C02 1:BBB:H01 1:BBB:C03
1:BBB:C04 1:BBB:H02 </beads>
</cg_bead>
................
Also I specified all <bonds> and <angles> and <weights>. It works
well, but the second nearest neighbor does not excluded from the rdf.
Seems that the exclusion works just for the first nearest neighbor. Is
it possible to exclude this interaction from the rdf?
On Jun 17, 11:11 am, Victor Rühle <rue...@votca.org> wrote:
> Hey,
>
> Can you please describe you problem in more details, what exactly did
> you try? Are you referring to calculating the target rdf, or the rdf in
> the iterations?
>
> We introduced proper exclusion handling in version 1.1, so it should
> work. You can check whether exclusions are read correctly by:
>
> csg_dump --top topol.tpr --excl
>
> or if you use csg_stat to calculate target rdf:
>
> csg_dump --top topol.tpr --cg mappin.xml --excl
>
> If you use g_rdf, you have to specify the topology -s topol.tpr in
> addition to an index file.
>
> A brief side-note:
> Be aware, that for the reference rdf and that during the iterations, the
> exact identical normalization should be used (there is room for some
> discrepancy, however as far as i could see it's more problematic for IMC
> than for IBI). Therefore better use the same program for both (csg_stat
> to calculate reference). In version 1.2, which was released yesterday,
> we have adjusted the normalization to be identical to g_rdf in gromacs 4.5.
>
> Victor
>
> On 06/17/2011 10:32 AM, chemistry wrote:
>
> > I have one addition question about the ibi procedure. I have a polymer
> > chain and I'm doing ibi for non-bonded interactions. How can I exclude
> > the bond part from the RDF? Because in my case I have all the same
> > beads in the backbone chain of my polymer and when I'm calculating the
> > RDF it does not correspond to the purely non-bond interactions. This
> > RDF except the non-bonded part includes the bonded part.
>
> > Thanks a lot in advance.
> > Sergio
>
> > On Jun 14, 2:59 pm, chemistry <donets1...@gmail.com> wrote:
> >> Thanks a lot for advice. Now ibi procedure works.
>
> >> On Jun 9, 8:31 pm, Victor Ruehle <rue...@votca.org> wrote:
>
> >>> Hey,
> >>> did you source your VOTCA installation?
> >>> source /votca-tools-1.1.1/bin/VOTCARC.bash
> >>> And if you manually installed gromacs that as well? If you still don"t
> >>> get it running
> >>> bash -x /votca-tools-1.1.1/bin/csg_inverse settings.xml
> >>> and send the output.
> >>> Cheers,
> >>> Victor
> >>> 2011/6/9 chemistry <donets1...@gmail.com>:
> >>>> Seems that yes. In the folder "/votca-tools-1.1.1/bin/" I have
> >>>> installed "csg_inverse" and all another tools.
> >>>> For installation of VOTCA I used "./build.sh". I installed
> >>>> additionally GROMACS with shared lib (*.so), because at the beginning
> >>>> it was a problem.
> >>>> On Jun 8, 1:38 pm, Christoph Junghans <jungh...@votca.org> wrote:
> >>>>> 2011/6/8 chemistry <donets1...@gmail.com>:> After run
> >>>>>> $ bash -x `which csg_inverse` settings.xml
> >>>>>> I've got this message:
> >>>>>> "bash: csg_inverse:: No such file or directory"
> >>>>> It seems like your installation is broken. How did you install your
> >>>>> VOTCA version?
> >>>>> Is there a csg_inverse installed?
> >>>>> Cheers,
> >>>>> Christoph
> >>>>>> I tried to set the path to the "csg_inverse" and gromacs directly in
> >>>>>> the "settings.xml" but it does not help.
> >>>>>> On Jun 7, 1:22 pm, Christoph Junghans <jungh...@votca.org> wrote:
> >>>>>>> 2011/6/7 chemistry <donets1...@gmail.com>:> Under "nothing happens" I
> >>>>>>> meant that after execution the command
> >>>>>>>> $ csg_inverse settings.xml (I'm using version 1.1.1)
> >>>>>>>> I have message: "end". And I do not have any created dir (step_000)
> >>>>>>>> or
> >>>>>>>> files (like inverse.log...).
> >>>>>>> Very strange! Please run
> >>>>>>> $ bash -x `which csg_inverse` settings.xml
> >>>>>>> and post the output.
> >>>>>>> Cheers,
> >>>>>>> Christoph
> >>>>>>>> But when I'm using
> >>>>>>>> $ csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg
> >>>>>>>> propane.xml
> >>>>>>>> for computing RDF's for propane it works with the same "settings.xml"
> >>>>>>>> file and I have created A-A.dist.new for A-A...
> >>>>>>>> Is it possible that I have some problem with a link to the gromacs
> >>>>>>>> and
> >>>>>>>> VOTCA cannot start iterative procedure?
> >>>>>>>> Thanks a lot in advance.
> >>>>>>>> Sergio
> >>>>>>>> On Jun 6, 10:56 am, Christoph Junghans <jungh...@votca.org> wrote:
> >>>>>>>>> Hi Sergio,
> >>>>>>>>> can you be a bit more explicit, what (not) happens?
> >>>>>>>>> I quickly tested the propane tutorial:
> >>>>>>>>> $ pwd
> >>>>>>>>> $HOME/votca/src/tutorials/propane/ibi
> >>>>>>>>> $ csg_inverse --options settings.xml #for version 1.1 remove
> >>>>>>>>> --options
> >>>>>>>>> For a more verbose log see: inverse.log
> >>>>>>>>> We are doing Method: ibi
> >>>>>>>>> Prepare (dir step_000)
> >>>>>>>>> Using initial guess from dist A-A.dist.tgt for A-A
> >>>>>>>>> ...
> >>>>>>>>> It seems to work for me.
> >>>>>>>>> Which version are you using? (see csg_stat --help)
> >>>>>>>>> Which command did you execute to start ibi?
> >>>>>>>>> Cheers,
> >>>>>>>>> Christoph
> >>>>>>>>> 2011/6/6 chemistry <donets1...@gmail.com>:
> >>>>>>>>>> Hello all!!!
> >>>>>>>>>> I'm just started to use votca and at the moment I'm going threw the
> >>>>>>>>>> tutorial. But I've got some problem with IBI procedure. In general
> >>>>>>>>>> I
> >>>>>>>>>> understood what mean every parameter in the "setting.xml" file but
> >>>>>>>>>> I
> >>>>>>>>>> have a problem when I'm trying to submit the calculation: nothing
> >>>>>>>>>> happened. Can anyone tell me what exactly I may have missed in the
> >>>>>>>>>> standart "setting.xml" file for propane. I'll appreciate any
> >>>>>>>>>> advise,
> >>>>>>>>>> thanks a lot in advance!
> >>>>>>>>>> Sergio
> >>>>>>>>>> --
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> >>>>>>>>> --
> >>>>>>>>> Dr. Christoph Junghans
> >>>>>>>>> Votca Core Developer
> >>>>>>>>> Web:http://www.votca.org
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> >>>>>>> Votca Core Developer
> >>>>>>> Web:http://www.votca.org
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> >>>>> Votca Core Developer
> >>>>> Web:http://www.votca.org
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