Hey Victor Thanks for uploading new tutorial files. Now fmatch works without error.
thanks sikandar On Thu, Oct 14, 2010 at 3:09 AM, Victor Ruehle <[email protected]> wrote: > 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 outdated, I uploaded a new version of tutorial tarball (and in 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]> > > > >>> > >>>>>> > >>> > >>>>>> <votca%[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]> > > > >>> > >>>>> > >>> > >>>>> <votca%[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]> > > > >>> > >>>> > >>> > >>>> <votca%[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]> > > > >>> > >>> > >>> > >>> <votca%[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. 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