Thanks Christoph.
I have noted the following error messages:
(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:
(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
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.
>
> > --
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>
> --
> Christoph Junghans
> Web:http://www.compphys.de- Hide quoted text -
>
> - Show quoted text -
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