Ok I will try that. Thank you. On Friday, March 3, 2017 at 4:42:12 PM UTC-6, Christoph Junghans wrote: > > 2017-03-03 15:31 GMT-07:00 Bijay Shrestha <[email protected] > <javascript:>>: > > 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? > Gromacs complains there is no table_ALC_CC.xvg, but you only have the > CC-ALC interaction in your settings.xml. > So I guess, you need to revert the order of "CC ALC" to "ALC CC" in > the energygrp_table line of your grompp.mdp. > Background here is that gromacs doesn't look for the Y-X table if only > the pair X-Y is list in the energygrp_table line. > > Christoph > > > > > > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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