Did you guys found any mistakes in my file? fyi I have made bonded interaction tables in table_b1, table_b2, table_a1.... xvg files which are numbered acc to CG topology file. I am supposed to do that instead of table_A_B.xvg for bonded interaction, right?
On Friday, March 3, 2017 at 9:18:02 AM UTC-6, Bijay Shrestha wrote: > > I re-ran the csg_inverse. Now it is asking for another file > table_ALC_CC.xvg. Same as above table_ALC_CC.xvg is the file I want to > create using csg_inverse. It creates table_CC_ALC.xvg in step_001 as > suggested in settings.xml. > > <non-bonded> > <!-- name of the interaction --> > <name>CC-ALC</name> > <!-- types involved in this interaction --> > <type1>CC</type1> > <type2>ALC</type2> > <!-- dimension + grid spacing of tables for calculations --> > <min>0</min> > <max>1.5</max> > <step>0.01</step> > <inverse> > <!-- target distribution (rdf), just give gromas rdf.xvg --> > <target>CC-ALC.dist.tgt</target> > <!-- update cycles --> > <do_potential>1 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_CC_ALC.xvg</table> > </gromacs> > </inverse> > </non-bonded> > > I have also attached my settings file and inverse.log. > > On Friday, March 3, 2017 at 8:44:20 AM UTC-6, Christoph Junghans wrote: >> >> 2017-03-02 13:13 GMT-07:00 Bijay Shrestha <[email protected]>: >> > Currently my error is (as shown in inverse.log) : >> > >> > Library file table_CC_DH1.xvg not found in current dir nor in default >> > directories. >> > (You can set the directories to search with the GMXLIB path variable) >> > For more information and tips for troubleshooting, please check the >> GROMACS >> > website at http://www.gromacs.org/Documentation/Errors >> > >> > However, this is the file I am trying to calculate using csg_inverse: >> > My settings files for the interaction looks like: >> > >> > <non-bonded> >> > <!-- name of the interaction --> >> > <name>CC-DH1</name> >> > <!-- types involved in this interaction --> >> > <type1>CC</type1> >> > <type2>DH1</type2> >> > <!-- dimension + grid spacing of tables for calculations --> >> > <min>0</min> >> > <max>1.5</max> >> > <step>0.01</step> >> > <inverse> >> > <!-- target distribution (rdf), just give gromas rdf.xvg --> >> > <target>CC-DH1.dist.tgt</target> >> > <!-- update cycles --> >> > <do_potential>1 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_CC_DH1.xvg</table> >> > </gromacs> >> > </inverse> >> > </non-bonded> >> > >> > What could be problem? And thank you for the support. >> Looks good so far! >> >> Is there a "table_CC_DH1.xvg" in your step_001? Can you attach your >> inverse.log? >> >> Christoph >> > >> > On Tuesday, February 28, 2017 at 4:14:47 PM UTC-6, Christoph Junghans >> wrote: >> >> >> >> 2017-02-28 15:08 GMT-07:00 Bijay Shrestha <[email protected]>: >> >> > Thank you for the help. It works now. My mistake was in my >> settings.xml >> >> > ( I >> >> > had an extra </nonbonded> in the file). However, I also faced >> another >> >> > problem. The problem now is that, suppose I have two beads namely A1 >> and >> >> > B1. >> >> > I have given dis.tgt for A1-B1. It is still asking me B1-A1 tables >> too. >> >> > Do I >> >> > need to have both interactions? A1-B1 and B1-A1 interactions >> mentioned? >> >> No, you just need one! See the propane example: >> >> >> >> >> https://github.com/votca/csg-tutorials/blob/master/propane/ibi/settings.xml >> >> it only has A-B. >> >> >> >> Christoph >> >> > >> >> > On Monday, February 27, 2017 at 3:39:09 PM UTC-6, Christoph Junghans >> >> > wrote: >> >> >> >> >> >> 2017-02-27 13:35 GMT-07:00 Bijay Shrestha <[email protected]>: >> >> >> > Hi there, >> >> >> > I had obtained bonded tabulated potentials for our study molecule >> >> >> > using >> >> >> > csg_boltzmann. Then using the tables of bonded potential, I am >> >> >> > working >> >> >> > on >> >> >> > the non-bonded interaction using csg_inverse. For this, I have >> edited >> >> >> > the >> >> >> > settings.xml and grompp.mdp, topol.top of propane tutorial for >> our >> >> >> > system. I >> >> >> > compared my files with the propane systems files for ibi run. >> >> >> > However, >> >> >> > when >> >> >> > I ran the csg_inverse --options settings.xml, it terminates >> >> >> > (prints"Terminated") without any error message or inverse.log. >> Could >> >> >> > you >> >> >> > help me answering what could I have been missing? >> >> >> 1.) Does the original tutorial work? (If not it might be a computer >> >> >> system issue). >> >> >> 2.) Make sure your settings.xml is a valid xml, check that with >> >> >> $ xmlwf settings.xml >> >> >> 3.) Run csg_inverse in debug mode: >> >> >> $ csg_inverse --debug --options settings.xml >> >> >> >> >> >> Christoph >> >> >> > >> >> >> > -- >> >> >> > 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. >> >> >> >> >> >> >> >> -- >> >> 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. >> >> >> >> -- >> 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.
