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. 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> >> <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]>< >> 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]> >> . >> 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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