2017-03-03 15:31 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > 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 <bijay.s...@selu.edu>: >>> > 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 <bijay.s...@selu.edu>: >>> >> > 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 <bijay.s...@selu.edu>: >>> >> >> > 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 votca+un...@googlegroups.com. >>> >> >> > To post to this group, send email to vo...@googlegroups.com. >>> >> >> > 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 votca+un...@googlegroups.com. >>> >> > To post to this group, send email to vo...@googlegroups.com. >>> >> > 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 votca+un...@googlegroups.com. >>> > To post to this group, send email to vo...@googlegroups.com. >>> > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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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