Am 15. Februar 2012 09:58 schrieb Tinashe <[email protected]>: > (Error 1) > $ awk -v kbt=1.6629 '{print $1, -kbt*log($2/$1/$1)}' > bond.dist.resample > bond.pot.ib > awk: (FILENAME=bond.dist.resample FNR=1) fatal: division by zero > attempted > > Using a file (bond.pot.ib) which I obtained from csg_boltzmann: Have you done the resampling like I did above. ( $csg_resample --in bond.dist.new --out bond.dist.resample --grid 0.154:0.001:0.179) As it crops away all point with y=0 and also x=0, which is why the command fails in your case.
> > (Error 2) > $ csg_call --options bond.xml --ia-type bond convert_potential gromacs > bond.pot.ib table_b1.xvg > Running subscript 'potential_to_gromacs.sh bond.pot.ib > table_b1.xvg'(from tags convert_potential gromacs) > Convert bond.pot.ib to table_b1.xvg > Running critical command 'mktemp bond.pot.smooth.XXXXX' > Running critical command 'csg_resample --in bond.pot.ib --out > bond.pot.smooth.18084 --grid 0:0.002: --comment Created on Wed Feb 15 > 17:43:06 CET 2012 > called from potential_to_gromacs.sh, version 1.2.1 hgid: 88d17d52748a > settings file: /tmp/tinashe/votca-tutorials-1.2.1/test_propane/ > atomistic_propane/bond.xml > working directory: /tmp/tinashe/votca-tutorials-1.2.1/test_propane/ > atomistic_propane' > wrong range format, use min:step:max > ################################################################################################################################################################################################### > # > ERROR: > # > # critical: 'csg_resample --in bond.pot.ib --out bond.pot.smooth.18084 > --grid 0:0.002: > called from potential_to_gromacs.sh, version 1.2.1 hgid: 88d17d52748a > settings file: /tmp/tinashe/votca-tutorials-1.2.1/test_propane/ > atomistic_propane/bond.xml > working directory: /tmp/tinashe/votca-tutorials-1.2.1/test_propane/ > atomistic_propane' failed # > # > ##################################################################################################################################################################################################Terminated > Strange. Which version of votca is that? There was a bug in that script in version 1.2.0, but you seem to have 1.2.1. Can you please post the output of $csg_property --file bond.xml --path cg.inverse.gromacs.table_end --short --print . and $csg_call --cat convert_potential gromacs Christoph > > The following is the bond.xml file (I have also changed the table_end > value to 3.0 but still get the same error): > $ cat bond.xml > <cg> > <inverse> > <program>gromacs</program> > <gromacs> > <pot_max>1e8</pot_max> > <table_end>0.3</table_end> > <table_bins>0.002</table_bins> > </gromacs> > </inverse> > </cg> > > > On Feb 14, 6:49 pm, Christoph Junghans <[email protected]> wrote: >> Hi Tinashe, >> >> I had another look at the tutorials and updated the fmatch.xml in >> propane/atomistic. >> It does change much, but it make it easier to come to the table in >> propane/ibi. >> >> So here is what I have done to get table_b1.xvg >> $csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --nt 5 >> --options fmatch.xml >> taken from run.sh, it creates bond.dist.new, which has only points, >> p>0 in the region 0.154 to 0.179. >> $csg_resample --in bond.dist.new --out bond.dist.resample --grid >> 0.154:0.001:0.179 >> This crops away the unimportant region >> $awk -v kbt=1.6629 '{print $1, -kbt*log($2/$1/$1)}' bond.dist.resample> >> bond.pot.ib >> >> (kbt=1.6629 as the propane example is done at T=200K) It does the >> Boltzmann inversion. >> $csg_call --options bond.xml --ia-type bond convert_potential gromacs >> bond.pot.ib table_b1.xvg >> If you plot table_b1.xvg in the region from 0.154 to 0.179 vs the >> table_b1.xvg in ibi you will see that they look pretty similar. >> Note1: the important region is the minimum + 2kbt. >> Note2: the table_b1.xvg in ibi folder is a hand-made table done in 2008. >> >> The rest of the deviation are due to technical things, which have >> changed since the VOTCA paper in 2009, which are: >> -extrapolation function (quadratic -> exponential) >> -interpolation function (cubic -> akima spline) >> -shift (none -> minimun to 0) >> >> Cheers, >> >> Christoph >> >> Am 13. Februar 2012 04:23 schrieb Tinashe <[email protected]>: >> >> >> >> >> >> > I have been trying to reproduce the table_*.xvg files in the propane >> > tutorial. >> >> > I obtained the bond potentials using csg_boltzmann: >> >> > The following are parts of the "bond.pot.ib" and "bond.xml" files: >> >> > "bond.pot.ib" >> > 0.152097 21.2962 5895.79 >> > 0.152405 19.4769 2445.97 >> > ... >> > 0.165675 0.0496598 149.931 >> > 0.165983 0.0142966 80.4637 >> > 0.166292 0 17.5345 >> > 0.1666 0.00347479 -44.5805 >> > 0.166909 0.0275138 -110.011 >> > ... >> > 0.180178 20.7073 -2300.42 >> > 0.180487 21.1912 -3816 >> >> > "bond.xml" >> > <cg> >> > <inverse> >> > <program>gromacs</program> >> > <gromacs> >> > <pot_max>1e8</pot_max> >> > <table_end>3</table_end> >> > <table_bins>0.002</table_bins> >> > </gromacs> >> > </inverse> >> > </cg> >> >> > I have done the following command to obtain the table_*.xvg file: >> >> > csg_call --options bond.xml --ia-type bonded convert_potential gromacs >> > bond.pot.ib table_b1.xvg >> >> > and read previous suggestions to Sergio for example concerning ibi >> > (https://groups.google.com/forum/#!msg/votca/OSaBKQTR7C0/wLAXmbGxw74J) >> > but I still can't get my table_b1.xvg to match the one in the >> > tutorial. I would really appreciate any help to resolve this issue. >> >> > Whilst the minimum point coincides, the right and left sides of the >> > potentials are very steep. >> >> > How is it that the tutorial file intercepts the vertical axis at >> > 6677.89??? >> > 0.000000 6677.890000 0 >> > 0.001000 6595.820000 0 >> > 0.002000 6514.250000 0 >> >> > I have tried to modify the bin size in the bond.xml and changed the >> > pot_max value but my table_b1.xvg file is still different??? I surely >> > have to be doing something wrong, please help me. >> >> > Thanks. >> >> > -- >> > 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 >> > athttp://groups.google.com/group/votca?hl=en. >> >> -- >> Christoph Junghans >> Web:http://www.compphys.de- Hide quoted text - >> >> - Show quoted text - > > -- > 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. > -- Christoph Junghans Web: http://www.compphys.de -- 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.
