Dear Sikandar, was a problem withj the input file. The fmatch.xml in spce was too outdated, I uploaded a new version of tutorial tarball (and in repository as well). Please update your files.
The problem is the missing option constrainedLS in the xml file.See here for help: http://www.votca.org/Documentation/reference-cgoptions Cheers, Victor 2010/10/14 Sikandar Mashayak <[email protected]>: > Hi > > After installing new votca along with gromacs4.5.1, csg_map does work well . > But running following command giving an error (as shown below) > > command > csg_fmatch --top topol.tpr --trj traj.trr --cg water.xml --options > fmatch.xml --begin 0 --nframes 30 > > output > > > Reading file topol.tpr, VERSION 4.5.1 (double precision) > I have 6540 beads in 2180 molecules > I have 2180 beads in 2180 molecules for the coarsegraining > trn version: GMX_trn_file (double precision) > Reading frame 0 time 0.000 > an error occured: > property not found: constrainedLS > > what does it mean? and how do I resolve it? > > thanks > sikandar > > On Wed, Oct 13, 2010 at 12:20 PM, Sikandar Mashayak <[email protected]> > wrote: >> >> great..this time votca ( with gromacs4.5.1) installed with just one >> command ./build.sh ..no errors no missing links... ;) >> >> thanks >> sikandar >> On Mon, Oct 11, 2010 at 2:52 AM, Victor Rühle <[email protected]> wrote: >>> >>> Yes :) ... but using the new gromacs version still might be a good >>> idea. >>> >>> On Oct 11, 5:37 am, Sikandar Mashayak <[email protected]> wrote: >>> > Hey Christoph >>> > >>> > To summarize , you are saying that if I link to Gromacs by adding >>> > -DGMX_DOUBLE to CPPFLAGS (keeping current gromacs) or upgrading gromacs >>> > then >>> > reinstalling VOTCA , probably newer release, will sort this issue. >>> > Right? >>> > >>> > In any of these options, I am guessing, I will have to reinstall VOTCA! >>> > >>> > thanks >>> > sikandar >>> > >>> > On Tue, Sep 28, 2010 at 9:48 AM, Christoph Junghans < >>> > >>> > [email protected]> wrote: >>> > > Hi Sikandar, >>> > >>> > > this is a combination of two things: >>> > >>> > > 1. to link against double precision gromacs you will have to add >>> > > -DGMX_DOUBLE to your CPPFLAGS. this is a known bug in gromacs-4.0.7, >>> > > which I >>> > > fixed a while ago in gromacs 4.5 and gromacs 4.0.8 (not released >>> > > yet), when >>> > > using pkg-config. My advice is to update your gromacs version. >>> > >>> > > Details for gromacs 4.0 here >>> > > < >>> > >>> > > >http://repo.or.cz/w/gromacs.git/commit/3b4d46a1abcc4c3b999febf8aa83a1...> >>> > >>> > > and for gromacs 4.5 here: >>> > > < >>> > >>> > > >http://repo.or.cz/w/gromacs.git/commit/053e0c52d9937eac9873ed2fa890e2... >>> > >>> > > 2.) There was a problem with the gmx 4.5 reader in votca-rc5 due to >>> > > some >>> > > changes in gromacs, which have been solved in the developer version >>> > > of >>> > > votca, so download it using Mercurial, see: >>> > > <http://code.google.com/p/votca/> >>> > > or wait until we have released votca-rc6 (expected for the end of the >>> > > week) >>> > >>> > > Cheers, >>> > >>> > > Christoph >>> > >>> > > Am 27.09.2010 22:04, schrieb Sikandar Mashayak: >>> > >>> > >> csg_map gives this error ... >>> > >>> > >> Reading file topol.tpr, VERSION 4.0.5 (double precision) >>> > >> Segmentation fault >>> > >>> > >> votca version .. >>> > >>> > >> csg_fmatch, version 1.0_rc5 hgid: cce356ff52dd (compiled May 20 >>> > >> 2010, >>> > >> 00:37:52) >>> > >> votca_tools, version 1.0_rc5 hgid: ed6908116baf (compiled May 20 >>> > >> 2010, >>> > >> 00:37:19) >>> > >> gromacs, VERSION 4.0.7 >>> > >>> > >> when I run csg_map with gdb , "bt" command after segmentation fault >>> > >> gives >>> > >> following msg. >>> > >>> > >> #0 GMXTopologyReader::ReadTopology (this=0x80551f0, file=..., >>> > >> top=...) >>> > >> at gmxtopologyreader.cc:67 >>> > >> #1 0xb7facd89 in CGEngine::Run (this=0xbfffeffc) at cgengine.cc:187 >>> > >> #2 0x0804c399 in main (argc=7, argv=0xbffff1b4) at csg_map.cc:109 >>> > >>> > >> thanks >>> > >> sikandar >>> > >>> > >> On Tue, Sep 21, 2010 at 10:18 AM, Victor Ruehle<[email protected]> >>> > >> wrote: >>> > >>> > >> Hey, >>> > >>> > >>> some checks: >>> > >>> > >>> - did you source the same gromacs version against which you >>> > >>> compiled >>> > >>> votca >>> > >>> - did you specify to write out forces in grompp file. it should be >>> > >>> nstxout = nstfout and you'll have to use the trr file, not trx >>> > >>> - does csg_map work? >>> > >>> - i see you are using double precision gromacs. There were some >>> > >>> issues >>> > >>> with malfunction gromacs defines in combination with double >>> > >>> precision, >>> > >>> could be an issue here... Which votca version are you using? >>> > >>> csg_fmatch --help should tell the version string including an >>> > >>> hgid... >>> > >>> - if the above didn't help,can you please send debug information: >>> > >>> gdb csg_fmatch (without any further parameters) >>> > >>> and then type >>> > >>> run<here the parameters you run fmatch with> >>> > >>> If it stops with segmentation fault, please type bt (for backtrace) >>> > >>> and post the output. >>> > >>> > >>> Cheers, >>> > >>> Victor >>> > >>> > >>> 2010/9/21 Sikandar Mashayak<[email protected]>: >>> > >>> > >>>> hey Victor, I am trying out the command csg_fmatch with the >>> > >>>> options you >>> > >>>> specified. I am using my own 4ns GROMACS MD data for topol.tpr >>> > >>>> and >>> > >>> > >>> traj.trr >>> > >>> > >>>> options, which I suppose should be fine. But I am getting this >>> > >>>> error... >>> > >>>> Reading file topol.tpr, VERSION 4.0.5 (double precision) >>> > >>>> Segmentation fault >>> > >>>> I get similar error when I try to run tutorial scripts for >>> > >>>> Propane.. >>> > >>>> Is there something wrong with my VOTCA installation or input files >>> > >>>> itself >>> > >>>> have errors! >>> > >>>> thanks >>> > >>>> sikandar >>> > >>>> On Tue, Sep 21, 2010 at 4:06 AM, Victor Ruehle<[email protected]> >>> > >>>> wrote: >>> > >>> > >>>>> Hey, >>> > >>>>> oh, yea. that's only the atomistic run. fmatching run is >>> > >>>>> misshing, but >>> > >>>>> just do after the atomistic run: >>> > >>> > >>>>> csg_fmatch --top topol.tpr --trj traj.trr --cg water.xml.xml >>> > >>>>> --options >>> > >>>>> fmatch.xml --begin 2000 --nframes<some-number> >>> > >>> > >>>>> where<some-number> depends on how long you want to wait/accuracy >>> > >>>>> you >>> > >>>>> want to get. For the first try someting around 30 should be ok, >>> > >>>>> then >>> > >>>>> increase later. >>> > >>> > >>>>> to get potetnials call csg_call table integrate (see recent >>> > >>>>> posts) >>> > >>> > >>>>> Cheers, >>> > >>>>> Victor >>> > >>> > >>>>> 2010/9/20 Sikandar Mashayak<[email protected]>: >>> > >>> > >>>>>> sorry forgot to provide the link of script file... which I am >>> > >>>>>> using to >>> > >>>>>> run >>> > >>>>>> FM algorithm ... >>> > >>> > >>> > >>> >>>http://hg.votca.org/hgwebdir.cgi/tutorials/file/d9b7ba3b777b/spce/ato... >>> > >>> > >>>>>> On Mon, Sep 20, 2010 at 4:12 PM, Sikandar Mashayak >>> > >>>>>> <[email protected]> >>> > >>>>>> wrote: >>> > >>> > >>>>>>> Hi >>> > >>>>>>> I am wondering whether the Force Matching tutorial script for >>> > >>>>>>> SPC/E >>> > >>>>>>> water >>> > >>>>>>> is complete? or is there any part of it is missing? >>> > >>>>>>> thanks >>> > >>>>>>> sikandar >>> > >>> > >>>>>> -- >>> > >>>>>> 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]<votca%[email protected]> >>> > >>>>>> >>> > >>>>>> <votca%[email protected]<votca%[email protected]> >>> > >>> > >>>>> . >>> > >>> > >>>> For more options, visit this group at >>> > >>>>>>http://groups.google.com/group/votca?hl=en. >>> > >>> > >>>>> -- >>> > >>>>> 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]<votca%[email protected]> >>> > >>>>> >>> > >>>>> <votca%[email protected]<votca%[email protected]> >>> > >>> > >>>> . >>> > >>> > >>>> For more options, visit this group at >>> > >>>>>http://groups.google.com/group/votca?hl=en. >>> > >>> > >>>> -- >>> > >>>> 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]<votca%[email protected]> >>> > >>>> >>> > >>>> <votca%[email protected]<votca%[email protected]> >>> > >>> > >>> . >>> > >>> > >>>> For more options, visit this group at >>> > >>>>http://groups.google.com/group/votca?hl=en. >>> > >>> > >>> -- >>> > >>> 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]<votca%[email protected]> >>> > >>> >>> > >>> <votca%[email protected]<votca%[email protected]> >>> > >>> >. >>> > >>> > >>> For more options, visit this group at >>> > >>>http://groups.google.com/group/votca?hl=en. >>> > >>> > > -- >>> > > Dipl.-Phys. Christoph Junghans >>> > > Max Planck Institute for Polymer Research >>> > > Theory Group >>> > > POBox 3148 >>> > > D 55021 Mainz, Germany >>> > >>> > > Phone: +49 6131 379 335 >>> > > >>> > > Web:http://www.mpip-mainz.mpg.de/~junghans<http://www.mpip-mainz.mpg.de/%7Ejunghans> >>> > >>> > > -- >>> > > 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] >>> > > <votca%[email protected]>. >>> > > For more options, visit this group at >>> > >http://groups.google.com/group/votca?hl=en. >>> > >>> > >>> >>> -- >>> 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 at >>> http://groups.google.com/group/votca?hl=en. >>> >> > > -- > 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 at > http://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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