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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