2016-05-16 16:00 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > After I included the simple pressure correction, it gives me an error > without inverse.log file. It just terminated. Without pressure correction, > IBI runs as usual. Would you give any trouble shooting advice? Hard to say, try running the example first!
Maybe your xml file has a syntax error, try: $ xmlwf settings.xml > > > running csg_inverse --options "settings.xml" > ./run.sh: line 4: 28777 Terminated csg_inverse --options > settings.xml > > > > > This is the part of settings.xml. The following reds are what I added. > > > <!-- example for a non-bonded interaction entry --> > <non-bonded> > <!-- name of the interaction --> > <name>A-A</name> > <!-- types involved in this interaction --> > <type1>A</type1> > <type2>A</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0.32</min> > <max>1.47</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>CG-CG.A-A.dist.tgt</target> > <p_target>1.0</p_target> > <!-- update cycles --> > <do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential> > <!-- additional post processing of dU before added to potential --> > <post_update>pressure</post_update> > <post_update_options> > <pressure> > <type>simple</type> > <do>0 1 1 1 1 1 1 1 1 1 1 1 1 1 1</do> > <simple> > <scale>0.0003</scale> > </simple> > </pressure> > </post_update_options> > <!-- additional post processing of U after dU added to potential --> > <post_add>convergence</post_add> > <!-- name of the table for gromacs run --> > <gromacs> > <table>table_A_A.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > > > Thank you. > > Best regards, > Changwoon Jang > > > > > On Mon, May 16, 2016 at 5:34 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2016-05-16 15:27 GMT-06:00 Chang Woon Jang <[email protected]>: >> > Dear Christoph, >> > >> > Thank you for the quick reply. In the spce/ibi_pressure example, >> > <do_potential> is every second step (ex., 0 1 0) and <do> inside >> > <pressure> >> > is every first and third step (1 0 1). >> > >> > >> > Do these <do_potential> and <do> alternatively need to be set? or Can I >> > set >> > as I wish as follows? >> You can set them as you wish! In the example we used them alternating. >> >> Christoph >> > >> > >> > >> > >> > >> > Thank you. <non-bonded> >> > <!-- name of the interaction --> >> > <name>A-A</name> >> > <!-- types involved in this interaction --> >> > <type1>A</type1> >> > <type2>A</type2> >> > <!-- dimension + grid spacing of tables for calculations --> >> > <min>0.32</min> >> > <max>1.47</max> >> > <step>0.01</step> >> > <inverse> >> > <!-- target distribution (rdf), just give gromas rdf.xvg --> >> > <target>CG-CG.A-A.dist.tgt</target> >> > <p_target>1.0</p_target> >> > <!-- update cycles --> >> > <do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 0 0</do_potential> >> > <!-- additional post processing of dU before added to potential >> > --> >> > <post_update>pressure</post_update> >> > <post_update_options> >> > <pressure> >> > <type>simple</type> >> > <do>1 0 1</do> >> > <simple> >> > <scale>0.0003</scale> >> > </simple> >> > </pressure> >> > </post_update_options> >> > <!-- additional post processing of U after dU added to potential >> > --> >> > <post_add>convergence</post_add> >> > <!-- name of the table for gromacs run --> >> > <gromacs> >> > <table>table_A_A.xvg</table> >> > </gromacs> >> > </inverse> >> > </non-bonded> >> > >> > >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > >> > >> > On Mon, May 16, 2016 at 5:05 PM, Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> 2016-05-16 15:00 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> > Dear VOTCA users, >> >> > >> >> > >> >> > I need a help to use pressure correction during nonbond IBI >> >> > calculation. Without the pressure correction, the derived CG >> >> > potentials >> >> > do >> >> > not give the right density close to experiment. The density is much >> >> > lower >> >> > than the experiment. Therefore, I would like to re-derive nonbond >> >> > potentials >> >> > using pressure correction. The previous setting.xml for nonbond IBI >> >> > is >> >> > like >> >> > below for example. Where do I need to put the <p_target>, >> >> > <post_update>, >> >> > <pressure>, <type>, etc? Do I need to put those blocks in the >> >> > <inverse> >> >> > block? >> >> > >> >> > I am not sure the syntax for the pressure correction. Would you >> >> > please >> >> > give >> >> > me a comment or example script? Thank you very much. >> >> See the spce/ibi_pressure tutorial: >> >> https://github.com/votca/csg-tutorials/tree/master/spce/ibi_pressure >> >> >> >> The p_target goes into the inverse block and the pressure block under >> >> the post_update_options option. >> >> >> >> Christoph >> >> > >> >> > <non-bonded> >> >> > <!-- name of the interaction --> >> >> > <name>A-A</name> >> >> > <!-- types involved in this interaction --> >> >> > <type1>A</type1> >> >> > <type2>A</type2> >> >> > <!-- dimension + grid spacing of tables for calculations --> >> >> > <min>0.32</min> >> >> > <max>1.47</max> >> >> > <step>0.01</step> >> >> > <inverse> >> >> > <!-- target distribution (rdf), just give gromas rdf.xvg --> >> >> > <target>CG-CG.A-A.dist.tgt</target> >> >> > <!-- update cycles --> >> >> > <do_potential>1 0 0 0 0 0 0 0 0 0 0 0 0 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>convergence</post_add> >> >> > <!-- name of the table for gromacs run --> >> >> > <gromacs> >> >> > <table>table_A_A.xvg</table> >> >> > </gromacs> >> >> > </inverse> >> >> > </non-bonded> >> >> > >> >> > >> >> > Best regards, >> >> > Changwoon Jang, >> >> > >> >> > -- >> >> > 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 https://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> -- >> >> 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 https://groups.google.com/group/votca. >> >> For more options, visit https://groups.google.com/d/optout. >> > >> > >> > -- >> > 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 https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> 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 https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > -- > 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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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