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/3b4d46a1abcc4c3b999febf8aa83a1260053a674>
and for gromacs 4.5 here:
<http://repo.or.cz/w/gromacs.git/commit/053e0c52d9937eac9873ed2fa890e2b273488c8f>
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/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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