2013/7/31 <[email protected]>:
> 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] wrote:
>> >> >>
>> >> >> 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
>> >> > Groups
>> >> > "votca" group.
>> >> > To unsubscribe from this group and stop receiving emails from it,
>> >> > 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
>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, 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
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, 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
--
You received this message because you are subscribed to the Google Groups
"votca" group.
To unsubscribe from this group and stop receiving emails from it, 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.
