Am 16. Februar 2012 01:08 schrieb Tinashe <tinashe.nd...@gmail.com>:
> Hi Christoph,
>
> When making the file "bond.dist.resample", the script automatically
> puts a "#" on the first line and this is what was causing the error:
> awk: (FILENAME=bond.dist.resample FNR=1) fatal: division by zero
> attempted
Sorry I used a never version of csg_resample. You can easily filter
away line starting with #
$ awk -v kbt=1.6629 '/^[^#]/{print $1, -kbt*log($2/$1/$1)}' >
bond.dist.resample > bond.pot.ib
/^[^#]/ means lines starting with any character but #.
> The following command gives the tabel_end value specified in bond.xml
> as output:
> $ csg_property --file bond.xml --path cg.inverse.gromacs.table_end --
> short --print .
> 0.3
>
> Your second request is as follows:
> $ csg_call --cat convert_potential gromacs
> #!/bin/bash
> ...
Both things look ok, which makes it hard to tell where this error comes from.
I would recommend to update to VOTCA 1.2.2 to see if the problem persists.
>
> To create the angle and dihedral potentials, are the following
> commands correct (I can email you the plots to have a more complete
> view)?:
Looks good!
>
> sed -e 's/$/ i/' BAB-angle.pot.ib | tac | sed -e '1,2d' | tac >
> BAB.cut
> csg_call table smooth BAB.cut BAB.smooth
> csg_resample --in BAB.smooth --out BAB.refined --grid
> 0::0.001:3.141592654
> csg_call table extrapolate --function sasha --region left BAB.refined
> BAB.refined
> csg_call table extrapolate --function sasha --region right BAB.refined
> BAB.refined
> awk '{print $1/3.141592654*180.0,$2}' BAB.refined > BAB.pot.cur
> csg_call --ia-type angle --ia-name BAB --options convert.xml
> convert_potential gromacs
>
> sed -e '1d' -e '$d' BBAB-dihedral.pot.ib > BBAB.cut
> #csg_call table smooth BBAB.cut BBAB.smooth <--- this command fails
You don't necessarily have to smooth the potential, only do that if is rough.
What was the error message here? (Update to Votca 1.2.2 first)
Christoph
> and I renamed BBAB.cut to BBAB.smooth to proceed to the next command
> csg_resample --in BBAB.smooth --out BBAB.refined --grid
> -3.141592654::0.001:3.141592654
> csg_call table extrapolate --function sasha --region left BBAB.refined
> BBAB.refined
> csg_call table extrapolate --function sasha --region right
> BBAB.refined BBAB.refined
> awk '{print $1/3.141592654*180.0,$2}' BBAB.refined > BBAB.pot.cur
> csg_call --ia-type dihedral --ia-name BBAB --options convert.xml
> convert_potential gromacs
>
> Thanks.
>
> Tinashe
> ---
>
> On Feb 15, 6:37 pm, Christoph Junghans <jungh...@votca.org> wrote:
>> Am 15. Februar 2012 09:58 schrieb Tinashe <tinashe.nd...@gmail.com>:> (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 <jungh...@votca.org> 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 <tinashe.nd...@gmail.com>:
>>
>> >> > 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
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