Thank you very much. It worked. My problem was because of the order of interactions in my grompp.mdp, as you mentioned. However, I got another error related to my bonded potential xvg file. Could you help me on it?
Fatal error: A tabulated bond interaction table number 18 is out of the table range: r 1.004090, between table indices 1004 and 1005, table length 1001 I had bonded interaction range of 0.6 nm. I got a similar error of being out of range but around r to be 0.6005. Hence I increased my table_end to 1.0 nm. However, I keep getting the same error. On Friday, March 3, 2017 at 8:02:40 PM UTC-6, Bijay Shrestha wrote: > > 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]>: >> > 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]. >> > 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.
