Thanks a lot for the previous advices! I have one more question about table_*.xvg. Can you explain please how exactly did you create all tables for the propane which you used for the ibi-procedure (table.xvg, table_a1.xvg, table_b1.xvg). I did the post-processing of the potentials (bond and angle) and I've got the same shape for the potentials but much more higher value for the y- axis. The distribution functions and potentials for bond and angle are the same like in your presentation. Did I do something wrong or is it something else what I should know? And which role plays table.xvg in this case?
Thanks a lot in advance, Sergio. On Jun 23, 11:34 am, Christoph Junghans <jungh...@votca.org> wrote: > Hi Sergio, > > 2011/6/22 chemistry <donets1...@gmail.com>:> 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? > > Usually one don't want to consider pairs of beads, which interact via > a bonded potential, for the rdf. > The reason is that the rdf is used to calculate the non-bonded > interaction and so only the pairs which interact non-bonded should go > in the rdf. > > However in some cases it is useful to calculate the rdf with different > exclusions than the simulation was performed. (the > cg.inverse.gromacs.rdf.topol option in the xml setting file, see the > manual) > > Cheers, > > Christoph > > > > > Thanks a lot in advance. > > Sergio > > > On Jun 21, 6:02 pm, Victor Ruehle <rue...@votca.org> 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 <donets1...@gmail.com>: > > >> > 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 <rue...@votca.org> 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 <donets1...@gmail.com> wrote: > >> >> >> Thanks a lot for advice. Now ibi procedure works. > > >> >> >> On Jun 9, 8:31 pm, Victor Ruehle <rue...@votca.org> 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 <donets1...@gmail.com>: > >> >> >>>> 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 <jungh...@votca.org> wrote: > >> >> >>>>> 2011/6/8 chemistry <donets1...@gmail.com>:> 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 <jungh...@votca.org> wrote: > >> >> >>>>>>> 2011/6/7 chemistry <donets1...@gmail.com>:> 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 <jungh...@votca.org> > >> >> >>>>>>>> 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 <donets1...@gmail.com>: > >> >> >>>>>>>>>> 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 > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to votca@googlegroups.com. To unsubscribe from this group, send email to votca+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
