Hey, Can you please describe you problem in more details, what exactly did you try? Are you referring to calculating the target rdf, or the rdf in the iterations?
We introduced proper exclusion handling in version 1.1, so it should work. You can check whether exclusions are read correctly by: csg_dump --top topol.tpr --excl or if you use csg_stat to calculate target rdf: csg_dump --top topol.tpr --cg mappin.xml --excl If you use g_rdf, you have to specify the topology -s topol.tpr in addition to an index file. A brief side-note: Be aware, that for the reference rdf and that during the iterations, the exact identical normalization should be used (there is room for some discrepancy, however as far as i could see it's more problematic for IMC than for IBI). Therefore better use the same program for both (csg_stat to calculate reference). In version 1.2, which was released yesterday, we have adjusted the normalization to be identical to g_rdf in gromacs 4.5. Victor On 06/17/2011 10:32 AM, chemistry wrote: > I have one addition question about the ibi procedure. I have a polymer > chain and I'm doing ibi for non-bonded interactions. How can I exclude > the bond part from the RDF? Because in my case I have all the same > beads in the backbone chain of my polymer and when I'm calculating the > RDF it does not correspond to the purely non-bond interactions. This > RDF except the non-bonded part includes the bonded part. > > Thanks a lot in advance. > Sergio > > On Jun 14, 2:59 pm, chemistry <[email protected]> wrote: >> Thanks a lot for advice. Now ibi procedure works. >> >> On Jun 9, 8:31 pm, Victor Ruehle <[email protected]> wrote: >> >>> Hey, >>> did you source your VOTCA installation? >>> source /votca-tools-1.1.1/bin/VOTCARC.bash >>> And if you manually installed gromacs that as well? If you still don"t >>> get it running >>> bash -x /votca-tools-1.1.1/bin/csg_inverse settings.xml >>> and send the output. >>> Cheers, >>> Victor >>> 2011/6/9 chemistry <[email protected]>: >>>> Seems that yes. In the folder "/votca-tools-1.1.1/bin/" I have >>>> installed "csg_inverse" and all another tools. >>>> For installation of VOTCA I used "./build.sh". I installed >>>> additionally GROMACS with shared lib (*.so), because at the beginning >>>> it was a problem. >>>> On Jun 8, 1:38 pm, Christoph Junghans <[email protected]> wrote: >>>>> 2011/6/8 chemistry <[email protected]>:> After run >>>>>> $ bash -x `which csg_inverse` settings.xml >>>>>> I've got this message: >>>>>> "bash: csg_inverse:: No such file or directory" >>>>> It seems like your installation is broken. How did you install your >>>>> VOTCA version? >>>>> Is there a csg_inverse installed? >>>>> Cheers, >>>>> Christoph >>>>>> I tried to set the path to the "csg_inverse" and gromacs directly in >>>>>> the "settings.xml" but it does not help. >>>>>> On Jun 7, 1:22 pm, Christoph Junghans <[email protected]> wrote: >>>>>>> 2011/6/7 chemistry <[email protected]>:> Under "nothing happens" I >>>>>>> meant that after execution the command >>>>>>>> $ csg_inverse settings.xml (I'm using version 1.1.1) >>>>>>>> I have message: "end". And I do not have any created dir (step_000) or >>>>>>>> files (like inverse.log...). >>>>>>> Very strange! Please run >>>>>>> $ bash -x `which csg_inverse` settings.xml >>>>>>> and post the output. >>>>>>> Cheers, >>>>>>> Christoph >>>>>>>> But when I'm using >>>>>>>> $ csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg >>>>>>>> propane.xml >>>>>>>> for computing RDF's for propane it works with the same "settings.xml" >>>>>>>> file and I have created A-A.dist.new for A-A... >>>>>>>> Is it possible that I have some problem with a link to the gromacs and >>>>>>>> VOTCA cannot start iterative procedure? >>>>>>>> Thanks a lot in advance. >>>>>>>> Sergio >>>>>>>> On Jun 6, 10:56 am, Christoph Junghans <[email protected]> wrote: >>>>>>>>> Hi Sergio, >>>>>>>>> can you be a bit more explicit, what (not) happens? >>>>>>>>> I quickly tested the propane tutorial: >>>>>>>>> $ pwd >>>>>>>>> $HOME/votca/src/tutorials/propane/ibi >>>>>>>>> $ csg_inverse --options settings.xml #for version 1.1 remove --options >>>>>>>>> For a more verbose log see: inverse.log >>>>>>>>> We are doing Method: ibi >>>>>>>>> Prepare (dir step_000) >>>>>>>>> Using initial guess from dist A-A.dist.tgt for A-A >>>>>>>>> ... >>>>>>>>> It seems to work for me. >>>>>>>>> Which version are you using? (see csg_stat --help) >>>>>>>>> Which command did you execute to start ibi? >>>>>>>>> Cheers, >>>>>>>>> Christoph >>>>>>>>> 2011/6/6 chemistry <[email protected]>: >>>>>>>>>> Hello all!!! >>>>>>>>>> I'm just started to use votca and at the moment I'm going threw the >>>>>>>>>> tutorial. But I've got some problem with IBI procedure. In general I >>>>>>>>>> understood what mean every parameter in the "setting.xml" file but I >>>>>>>>>> have a problem when I'm trying to submit the calculation: nothing >>>>>>>>>> happened. Can anyone tell me what exactly I may have missed in the >>>>>>>>>> standart "setting.xml" file for propane. I'll appreciate any advise, >>>>>>>>>> thanks a lot in advance! >>>>>>>>>> Sergio >>>>>>>>>> -- >>>>>>>>>> You received this message because you are subscribed to the Google >>>>>>>>>> Groups "votca" group. >>>>>>>>>> To post to this group, send email to [email protected]. >>>>>>>>>> To unsubscribe from this group, send email to >>>>>>>>>> [email protected]. >>>>>>>>>> For more options, visit this group >>>>>>>>>> athttp://groups.google.com/group/votca?hl=en. >>>>>>>>> -- >>>>>>>>> Dr. Christoph Junghans >>>>>>>>> Votca Core Developer >>>>>>>>> Web:http://www.votca.org >>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "votca" group. >>>>>>>> To post to this group, send email to [email protected]. >>>>>>>> To unsubscribe from this group, send email to >>>>>>>> [email protected]. >>>>>>>> For more options, visit this group >>>>>>>> athttp://groups.google.com/group/votca?hl=en. >>>>>>> -- >>>>>>> Dr. Christoph Junghans >>>>>>> Votca Core Developer >>>>>>> Web:http://www.votca.org >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "votca" group. >>>>>> To post to this group, send email to [email protected]. >>>>>> To unsubscribe from this group, send email to >>>>>> [email protected]. >>>>>> For more options, visit this group >>>>>> athttp://groups.google.com/group/votca?hl=en. >>>>> -- >>>>> Dr. Christoph Junghans >>>>> Votca Core Developer >>>>> Web:http://www.votca.org >>>> -- >>>> You received this message because you are subscribed to the Google Groups >>>> "votca" group. >>>> To post to this group, send email to [email protected]. >>>> To unsubscribe from this group, send email to >>>> [email protected]. >>>> For more options, visit this group >>>> athttp://groups.google.com/group/votca?hl=en. >> -- You received this message because you are subscribed to the Google Groups "votca" group. 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