2013/8/1 <[email protected]>: > 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? Change it back to what it was or change it to -9.
> > Steven > > > On Wednesday, July 31, 2013 4:29:16 PM UTC+1, Christoph Junghans wrote: >> >> 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. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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