On Tue, Apr 3, 2018 at 11:05 PM, Alexander Alexander <alexanderwie...@gmail.com> wrote: > Thank you Christoph. > > The gmx_mpi mdrun crashed in the step_001, with the below error; > > Tabulated interaction of type 'Tab. Bonds' or 'Tab. Bonds NC' with index 0 > cannot be used because no table file whose name matched '_b0.xvg' was passed > via the gmx mdrun -tableb command-line option. Yeah, there was a bug in gromacs-5.1 and since then you need to explicitly use "-tableb" in mdrun call. Usually VOTCA adds that automatically except if you have done it manually in settings xml file. It seems, you mis-numbered the tables in your topol.top: [ bonds ] 1 2 8 0 1 ; 1:bond-LG-H:1 2 3 8 1 1 ; 1:bond-H-L:1 3 4 8 1 1 ; 1:bond-L-RG:1 says you need a table_b0.xvg and table_b1.xvg (4th column is the table number - you using 0 and 1), but then you referring to table_b1.xvg, table_b2.xvg and table_b3.xvg in your settings.xml, so something is wrong here.
(See the hexane/ibi_all for tutorial for details) > > But, it worked when I added "-tableb table_b0.xvg table_b1.xvg table_b2.xvg > table_a0.xvg table_a1.xvg" to the gmx_mpi mdrun, I was surprised because it > had thought the -tableb is kind of default when one intend to use tabulated > potential calming in case.mdp file. (gromacs2018.1). As you aren't referring to table_b0.xvg anywhere in your settings.xml file, I am not sure where this table is coming from. > > More questions; > > Similar to the normal atomistic simulation, I was wondering if the > minimization and equalization are needed for IBI (bonded and nonbonded) > prior to the sd simulation in each step? VOTCA can do both, a minimization can be done before the main simulation (see the spce/simplex/simple example). For equalization, just set the <equi_time> in the xml file to something bigger than 0 and VOTCA will skip these parts of the simulation (similar to gmx's -b option) But if you need one of the two options is system dependent. > > By csg_map one can map the atomistic.trr to CG.xtc, what could be the usage > of CG.txc in IBI (bonded and nonbonded) then? E.g. if you want to calculate some other properties of the CG system with gmx's tools, like diffusion constant. > > Should the conf.gro used in IBI be correspond to the conf.gro used in the > all atom simulation? To be clear, if the CG.gro used in IBI must be exactly > the one obtained by mapping the AA.gro and can not be bigger than that? Can > we make the CG.gro obtained by mapping twice to use it in IBI? Actually it is very common to scale up the system for IBI to get more statistics. And you don't have to use exactly the same starting configuration, but you should use one which is equilibrated (which is the case for mapped ones.) > > In using gmx rdf, we usually compare a selection (-sel) like A with a > reference (-ref) like B, and this means rdf_A_B.xvg might differ with the > situation where we switch the reference and selection to have rdf_B_A.xvg. > So, should we also consider this in for example csg_stat in setting,xml or > map.xml? in other words, should we define both <nonbonded> A B </nonbonded> > and <nonbonded> B A </nonbonded>? Honestly, there is only one interaction between A and B, so why would you calculate two RDFs? Also the way csg_stat calculates RDFs is symmetric. Christoph > > Thanks for your time in advance. > > Best regards, > Alex > > On Tuesday, April 3, 2018 at 5:29:00 AM UTC-4, Christoph Junghans wrote: >> >> >> >> On Tue, Apr 3, 2018, 09:31 Alexander Alexander <alexand...@gmail.com> >> wrote: >>> >>> Dear all, >>> >>> I am iterating over the both bonded and nonbonded interactions in my >>> system using IBI. I also let program to guess all the initial potential in >>> step_000. So, I do not need any external potential, but the program crashes >>> in the step_001 requiring a table.xvg, I have attached my input files in a >>> zip file, I would be so appreciated if you could have a look and help me >>> overcome the problem. >> >> >> I was wrong, the table.xvg is still needed even with gromacs-2016. So just >> create a table.xvg with all zeros as y columns (or copy one over from one of >> tutorials) >> >> See the gromacs manual on details for the table format of table.xvg! >> >> Christoph >> >>> >>> >>> Thank you. >>> >>> Best regards, >>> Alex >>> >>> -- >>> 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. > > -- > 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. 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.
