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 >> > >> > -- >> > 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]. >> > 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]. >> 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]. > 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]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
