Hey, Victor! Thanks a lot for advice, I checked all again and I found the mistake in my mappin.xml file. I fixed it and now it works well. Is it something important in the calculation of the rdf in the iterations for such a systems?
Thanks a lot in advance. Sergio On Jun 21, 6:02 pm, Victor Ruehle <[email protected]> wrote: > Hmm, are you sure that all the beads which should be excluded are > part of an angle definition? If yes, Votca should exclude them > automatically.. > > I'm doing a very similar thing and it worked for me. Will check > tomorrow whether there might be a new bug.However, third or fourth > nearest neighbors should still be visible, there is no option so far > to exclude all beads in the molecule. I could add that if necessary. > > Please verify if the peaks you observe really correspond to second > nearest neighbors, and if yes whether you have this particular angle > defined in the mapping. Also check csg_dump --excl > > 2011/6/21 chemistry <[email protected]>: > > > I'm trying to calculate the target rdf for polymer system with the > > "csg_stat" and also I'm interested to calculate the rdf in the > > iterations: > > > csg_stat --top topol.tpr --trj traj.xtc --options settings.xml --cg > > mapping.xml > > > I have P3HT system. Every monomer divided on the three beads. > > Thiophene ring represented the first bead and hexyl chain divided on > > the two beads - each bead include three carbon atoms. > > > in the settings.xml file I specified the types of the beads which are > > the same like in the mapping.xml: > > > ............. > > <non-bonded> > > <!-- name of the interaction --> > > <name>P1-P1</name> > > <!-- types involved in this interaction --> > > <type1>A</type1> > > <type2>A</type2> > > <!-- dimension + grid spacing of tables for calculations --> > > <min>0</min> > > <max>1.36</max> > > <step>0.01</step> > > <inverse> > > <!-- target distribution (rdf), just give gromas rdf.xvg --> > > <target>P1-P1.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></post_add> > > <!-- name of the table for gromacs run --> > > <gromacs> > > <table>table_P1_P1.xvg</table> > > </gromacs> > > </inverse> > > </non-bonded> > > ............... > > > ---mapping.xml---: > > > <cg_molecule> > > <name>P3HT</name> > > <ident>Protein_X</ident> > > <topology> > > <cg_beads> > > <cg_bead> > > <name>S1</name> > > <type>A</type> > > <symmetry>1</symmetry> > > <mapping>A</mapping> > > <beads> 1:BBB:S01 1:BBB:C01 1:BBB:C02 1:BBB:H01 1:BBB:C03 > > 1:BBB:C04 1:BBB:H02 </beads> > > </cg_bead> > > ................ > > > Also I specified all <bonds> and <angles> and <weights>. It works > > well, but the second nearest neighbor does not excluded from the rdf. > > Seems that the exclusion works just for the first nearest neighbor. Is > > it possible to exclude this interaction from the rdf? > > > On Jun 17, 11:11 am, Victor Rühle <[email protected]> wrote: > >> 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. > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. 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