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/atomistic/run.sh
> >> >
> >> >
> >> > 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
> >> >
> >> > --
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