Thank you. I added 2 - as you suggested but then get the error:
ERROR:
#
# critical: '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' failed #
--12 could not be convert to a number
Would you advise?
Steven
On Wednesday, July 31, 2013 4:29:16 PM UTC+1, Christoph Junghans wrote:
>
> 2013/7/31 <[email protected] <javascript:>>:
> > 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?
> Well VOTCA cannot know if you have named your energy group in the same
> ways as the types in the xml, hense there is a warning.
>
> > 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
> If you have multiple cores available, multi_g_rdf will calculate the
> rdf in parallel and calculate the average in the end.
> As a side effect, this will give you error bars on rdf, too.
>
> However it seems, there is a bug in that old script if you have more
> than 10 cores, you have 12 as I see from above.
> In the line of multi_g_rdf call change "-${tasks}" to "--${tasks}"
> with 2 - signs.
>
> diff -r 677c9083d714 share/scripts/still_dirty/calc_rdf_gromacs.sh
> --- a/share/scripts/still_dirty/calc_rdf_gromacs.sh Tue Jul 30
> 14:03:17 2013 -0600
> +++ b/share/scripts/still_dirty/calc_rdf_gromacs.sh Wed Jul 31
> 09:27:16 2013 -0600
> @@ -65,7 +65,7 @@
> else
> msg "Running g_rdf for ${grp1}-${grp2} using $tasks tasks"
> if [ $tasks -gt 1 ]; then
> - echo -e "${grp1}\n${grp2}" | critical multi_g_rdf --cmd ${g_rdf}
> -${tasks} -b ${begin} -e ${end} -n "$index" -o ${name}.dist.new.xvg
> --soutput ${name}.dist.new.NP.xvg -- -bin ${binsize} -s "$tpr" -f
> "${traj}" ${opts}
> + echo -e "${grp1}\n${grp2}" | critical multi_g_rdf --cmd ${g_rdf}
> --${tasks} -b ${begin} -e ${end} -n "$index" -o ${name}.dist.new.xvg
> --soutput ${name}.dist.new.NP.xvg -- -bin ${binsize} -s "$tpr" -f
> "${traj}" ${opts}
> else
> echo -e "${grp1}\n${grp2}" | critical ${g_rdf} -b ${begin} -n
> "$index" -bin ${binsize} -o ${name}.dist.new.xvg -s "$tpr" -f
> "${traj}" ${opts}
> fi
>
> Or replace the multi_g_rdf call with the normal g_rdf call for below.
>
> >
> > 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]>:
> >> > 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
> >> >> >>
> >> >> >>
> >> >> > --
> >> >> > You received this message because you are subscribed to the Google
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> >> >> > "votca" group.
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> >> >> > send
> >> >> > an
> >> >> > email to [email protected].
> >> >> > To post to this group, send email to [email protected].
> >> >> > Visit this group at http://groups.google.com/group/votca.
> >> >> > For more options, visit https://groups.google.com/groups/opt_out.
> >> >> >
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >
> >> > --
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> >> > To unsubscribe from this group and stop receiving emails from it,
> send
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> >> > email to [email protected].
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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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