Hi Sergio,
the potentials have to look similar around the minimum. The region
left and right are usually extrapolated and the exact form of the
extrapolation does not matter much as the appearance of these values
is exponentially suppressed (exp -E/k_bT).
Make sure that the area {U_min..U_min+k_b T} is correct.
Technically what I do to obtain table_b1.xvg is:
-calculate the distribution with csg_stat / csg_boltzmann
-calculate the potential using awk
$ awk -v kbt=NUMBER '{print $1,($1>0)?-kbt*log($2/$1/$1):"nan"}'
bond.dist.new > bond.pot.new
-take a look at the potential and cut it down to the well-sampled region
-convert it to gromacs format (this was reworked in VOTCA 1.2, before
the extrapolation had to be done by hand)
$ csg_call --options bond.xml --ia-type bonded convert_potential
gromacs bond.pot.new2 table_b1.xvg
where bond.xml looks like this:
<cg>
<inverse>
<program>gromacs</program>
<gromacs>
<pot_max>1e8</pot_max>
<table_end>3</table_end>
<table_bins>0.002</table_bins>
</gromacs>
</inverse>
</cg>
table.xvg is used to calculate the interactions for all pairs, which
do not appear in energygrp_table (in the mdp file).
If all pairs are covered by energygrp_table combinations you can use
any table, but I would use a table filled with zeros.
table.xvg can be useful in cases when you want to mix IBI tables with
a standard force field, then table.xvg should be the default 6-12 LJ
table ($GMXDATA/gromacs/top/table6-12.xvg)
Cheers,
Christoph
2011/6/26 chemistry <[email protected]>:
> Thanks a lot for the previous advices!
>
> I have one more question about table_*.xvg. Can you explain please how
> exactly did you create all tables for the propane which you used for
> the ibi-procedure (table.xvg, table_a1.xvg, table_b1.xvg). I did the
> post-processing of the potentials (bond and angle) and I've got the
> same shape for the potentials but much more higher value for the y-
> axis. The distribution functions and potentials for bond and angle are
> the same like in your presentation. Did I do something wrong or is it
> something else what I should know? And which role plays table.xvg in
> this case?
>
> Thanks a lot in advance,
> Sergio.
>
> On Jun 23, 11:34 am, Christoph Junghans <[email protected]> wrote:
>> Hi Sergio,
>>
>> 2011/6/22 chemistry <[email protected]>:> Thanks a lot for advice, I
>> checked all again and I found the mistake
>> > in my mappin.xml file. I fixed it and now it works well.
>> > Is it something important in the calculation of the rdf in the
>> > iterations for such a systems?
>>
>> Usually one don't want to consider pairs of beads, which interact via
>> a bonded potential, for the rdf.
>> The reason is that the rdf is used to calculate the non-bonded
>> interaction and so only the pairs which interact non-bonded should go
>> in the rdf.
>>
>> However in some cases it is useful to calculate the rdf with different
>> exclusions than the simulation was performed. (the
>> cg.inverse.gromacs.rdf.topol option in the xml setting file, see the
>> manual)
>>
>> Cheers,
>>
>> Christoph
>>
>>
>>
>> > Thanks a lot in advance.
>> > Sergio
>>
>> > On Jun 21, 6:02 pm, Victor Ruehle <[email protected]> wrote:
>> >> Hmm, are you sure that all the beads which should be excluded are
>> >> part of an angle definition? If yes, Votca should exclude them
>> >> automatically..
>>
>> >> I'm doing a very similar thing and it worked for me. Will check
>> >> tomorrow whether there might be a new bug.However, third or fourth
>> >> nearest neighbors should still be visible, there is no option so far
>> >> to exclude all beads in the molecule. I could add that if necessary.
>>
>> >> Please verify if the peaks you observe really correspond to second
>> >> nearest neighbors, and if yes whether you have this particular angle
>> >> defined in the mapping. Also check csg_dump --excl
>>
>> >> 2011/6/21 chemistry <[email protected]>:
>>
>> >> > 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 <[email protected]> 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 <[email protected]> wrote:
>> >> >> >> Thanks a lot for advice. Now ibi procedure works.
>>
>> >> >> >> On Jun 9, 8:31 pm, Victor Ruehle <[email protected]> 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 <[email protected]>:
>> >> >> >>>> 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 <[email protected]> wrote:
>> >> >> >>>>> 2011/6/8 chemistry <[email protected]>:> 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 <[email protected]>
>> >> >> >>>>>> wrote:
>> >> >> >>>>>>> 2011/6/7 chemistry <[email protected]>:> 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 <[email protected]>
>> >> >> >>>>>>>> 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 <[email protected]>:
>> >> >> >>>>>>>>>> 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
>> >> >> >>>>>>>>>> --
>> >> >> >>>>>>>>>> You received this message because you are subscribed to the
>> >> >> >>>>>>>>>> Google Groups "votca" group.
>> >> >> >>>>>>>>>> To post to this group, send email to
>>
>> ...
>>
>> read more »
>
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--
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Votca Core Developer
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