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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Web: http://www.compphys.de
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