On Mar 4, 2017 06:23, "Bijay Shrestha" <[email protected]> wrote:
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. That usually means your system is exploding and hence the bonded table are never long enough. You could try to fix some of the interactions first and only one iterate some. Christoph 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/i >> bi/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. -- 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.
