Dear Christoph, I found what the problem is. Too many lines of xml file make me difficult to find the syntax error. I really appreciate your help and patience for all my questions.
Best regards, Changwoon Jang On Mon, May 16, 2016 at 6:09 PM, Christoph Junghans <[email protected]> wrote: > 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. > 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.
