Done, thank you. Now I am stuck with:
Using given table CC.pot.in for CC
################################################################################################################################
#
#
#
ERROR:
#
# potential_extrapolate.sh: please specify add potential type (--type
options) from: non-bonded bond thermforce angle dihedral #
# For details see the logfile
/home/valentina/CG/inverse.log
#
#
#
################################################################################################################################
Terminated
I am not sure where to add this. I have added like this to every
interaction:
<bonded>
<name>CC</name>
<min>0</min>
<max>4</max>
<step>0.01</step>
<inverse>
<target>CC.dist.tgt</target>
<do_potential>1 0 0 0 </do_potential>
<post_update>scale</post_update>
<post_update_options>
<scale>0.1</scale>
</post_update_options>
<post_update>pressure</post_update>
<post_update_options>
<pressure>
<type>simple</type>
<do> 1 0 0 0</do>
<simple>
<scale>0.0001</scale>
</simple>
</pressure>
</post_update_options>
* <post_update_options>
<extrapolate> --type bond </extrapolate>
</post_update_options>*
<post_add></post_add>
<gromacs>
<table>table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
But it doesn't seem to pick up the input.
Also the programm asked me to provide CC.pot.in
I was not sure what is this potential, so I provided CC-bond.pot.ib (the
output from csg_boltzmann) - is this right?
Thank you very much,
V
On Friday, September 28, 2012 2:07:44 PM UTC+1, Valentina wrote:
>
> Hello!
>
> I am a little confused here.
>
> I have read somewhere that Votca 1.3 (? I thought latest version is 1.2.3)
> supports IBI for bonded - is this right?
>
> If so, how do I implement it? I have attatched my settings file (saved in
> .odt,but used as .xml on the machine). This doesn't seem to do more then
> fitting the nonbonded C-C potential. Am I missing something?
>
> Many thanks!
> Valentina
>
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