Hello, thank you again for the support. I have a last question. I used this
script to calculate RDF via gromacs g_rdf
In my xml
<non-bonded>
<name>ACI-ACI</name>
<type1>ACI</type1>
<type2>ACI</type2>
<min>0</min>
<max>3.5</max>
<step>0.05</step>
<inverse>
<target>ACI-ACI.dist.tgt</target>
<do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential>
<post_update></post_update>
<post_add>convergence</post_add>
<gromacs>
<grp1>ACI</grp1>
<grp2>ACI</grp2>
<table>table_ACI_ACI.xvg</table>
</gromacs>
</inverse>
</non-bonded>
I get a warining:
WARNING (in calc_rdf_generic.sh): could not find energy group of type1
(interaction property gromacs.grp1) using bead type1 (ACI) as failback !
then I see that from the index file Votca choose correct index group:
unning critical command 'multi_g_rdf --cmd g_rdf -12 -b 10 -e 1000 -n
index.ndx -o ACI-ACI.dist.new.xvg --soutput ACI-ACI.dist.new.NP.xvg -- -bin
0.05 -s topol.tpr -f traj.xtc -fade 3.5'
Select a reference group and 1 group
Group 0 ( System )
Group 1 ( Protein )
Group 2 ( Protein-H )
Group 3 ( C-alpha )
Group 4 ( Backbone )
Group 5 ( MainChain )
Group 6 ( MainChain+Cb )
Group 7 ( MainChain+H )
Group 8 ( SideChain )
Group 9 ( SideChain-H )
Group 10 ( ACI )
Group 11 ( BAS )
Group 12 ( POL )
Group 13 ( NON )
Group 14 ( GLY )
Select a group: Select a group:
Selected: ACI
ACI
Is that correct?
And why rdf s divided by into parts: e.g.
Calculation of rdf from 10 ps to 505 ps started (pid 15690, logfile
ACI-ACI.dist.new_00.log)
Calculation of rdf from 505 ps to 1000 ps started (pid 15694, logfile
ACI-ACI.dist.new_01.log)
Waiting for single rdf calculations to finish
Checking output
Calculating average
Thank you for your help!
Steven
W dniu czwartek, 25 lipca 2013 16:40:37 UTC+1 użytkownik Christoph Junghans
napisał:
>
> 2013/7/25 <[email protected] <javascript:>>:
> > I did what you have written copying the file from 2011 to the "scripts"
> > folder and I got the error and creating csg_table. I also added option
> -fade
> > 2.0 in xml file gromacs.g_rdf.opts and when running:
> >
> > # ERROR:
> > #
> > # do_external: subscript
> >
> /home/ps/ps-fs2/jkm210/Polyglycine/CHANDLER/IBI_METHOD/WCA_probeb4_IBI/scripts/my_rdf.sh
>
>
> > (from tags rdf gromacs) failed #
> >
> > WORK/IBI_METHOD/WCA_probeb4_IBI/scripts/my_rdf.sh: Permission denied
> You have to make the script executable:
> $ chmod u+x my_rdf.sh
>
> >
> > Would you suggest something please?
> >
> > Steven
> >
> >
> >
> >
> >
> > On Thursday, July 25, 2013 3:55:08 PM UTC+1, Christoph Junghans wrote:
> >>
> >> 2013/7/25 <[email protected]>:
> >> > And how g_rdf tool of gromacs will know which groups to use from
> >> > index.ndx ?
> >> That was one of the reason to deprecate g_rdf and make csg_stat the
> >> default. VOTCA uses types not energy groups.
> >>
> >> Back in 2011, we used the following script:
> >>
> >> <
> https://code.google.com/p/votca/source/browse/share/scripts/inverse/calc_rdf_gromacs.sh?repo=csg&name=a3e6095e3ee6>
>
>
> >> This could serve as basis for your myrdf.sh
> >> >
> >> > Steven
> >> >
> >> >
> >> > On Monday, July 15, 2013 12:02:00 PM UTC+1, [email protected]:
> >> >>
> >> >> Dear Votca Users,
> >> >>
> >> >> I have to issues with IBI:
> >> >>
> >> >> 1) I took one my ditributions and calculated on my own potential W=
> >> >> -kBT
> >> >> ln(RDF) and I got different potential than Votca provide me. For
> >> >> instance
> >> >> lets calculate the potential minimum for the distribution maximum of
> >> >> 162.
> >> >> Pot = -.249435*ln(164) = -12.69. The minimum of Votca potential
> >> >> corresponds
> >> >> to approximately -16 kJ/mol. Where I missed something? is it somehow
> >> >> normalized?
> >> >>
> >> >> 2) After 1st iteration my distribution was much higher than the
> target
> >> >> one
> >> >> so I guess the potential should decrease but apparently the new
> >> >> potential
> >> >> has deeper minima so the next distribution has a even higer
> >> >> distribution.
> >> >> Could anyone please explain me this?
> >> >>
> >> >> Steven
> >> >>
> >> >>
> >> > --
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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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