2013-10-09 10:42 GMT-06:00 Chandan Choudhury <[email protected]>:
> Dear votca users,
>
> I would like to share my experience regarding the iteration of bonded
> interactions.
>
> I prefer to use the following script for iterating the bonds:
What is the advantage of that script over the bonded IBI in VOTCA 1.3?
Most of the stuff below can be done as post-update script as well.
>
> For the first iteration, I used the tabulated potentials generated from the
> csg_boltzmann. Upon its completion, I used the following scripts:
Some comments below:
>
> #!/bin/sh
> i_in=1
> if [ "$#" -ne 0 ]; then
"$#" is "number of arguments"! Does that make sense?
> echo $#
> cd step_00$i_in
> echo `pwd`
Simply use pwd instead.
> mkdir tables
> mv $1.bond.pot.cur $1.bond.pot.cur_I
> sed -e '1,4d' -e 's/$/ i/' $1.bond.pot.new | tac | sed -e '1,3d' | tac
>> $1.bond.cut
Use
$ csg_call table change_flag $1.bond.pot.new $1.bond.cut
instead
>
> source /opt/apps/votca/1.2.3/bin/VOTCARC.bash
> source /opt/apps/gmx/single/463/bin/GMXRC
> csg_call table smooth $1.bond.cut $1.bond.smooth
> csg_resample --in $1.bond.smooth --out $1.bond.refined --grid
> 0::0.001:0.5
Simply add "smooth" to the post_update list of the "bond" interaction
(see spce/realtime example)
> csg_call table extrapolate --function quadratic $1.bond.refined
> $1.bond.pot.cur
same here, add "extrapolate" to the post_update list of the "bond" interaction.
> csg_call --ia-type bonded --ia-name $1.bond --options ../convert.xml
> convert_potential gromacs
>
> cd ..
> rm 'done'
> i_c=`expr $i_in + 1`
> sed -i s/iterations_max\>$i_in/iterations_max\>$i_c/ settings.xml
> sh run.sh
Instead of the above four lines, simply set iterations_max=0 in
settings.xml and call
$ csg_inverse --do-iterations 1 --options settings.xml
to do one iteration at the time.
> fi
>
> The i_in is the variable which is the iteration step.
> These commands generate tabulated potentials for the bond type. Then this
> tabulated potential is the input for the next iteration. (What I did was I
> stopped the the iteration with the simulation by gromacs starts. Then copy
> the tabulated potential for the earlier step and again execute run.sh)
>
> The above script comes into picture if there is bad sampled region in the
> new potential. The bad sampled region is manually identified and the values
> goes as an input in the sed command. The region is cut and then other
> commands follow. I use 1.2.3 for this purpose and 1.3-dev gets sourced in
> the run.sh.
> Here, I iterated one bond and then 2nd and so on.
>
> The same procedure is followed for generating optimized potentials for
> angles.
>
> #!/bin/sh
> i_in=3
> if [ "$#" -ne 0 ]; then
> echo $#
> cd step_00$i_in
> echo `pwd`
> mkdir tables
> mv $1.angle.pot.cur $1.angle.pot.cur_I
> sed -e '1,17d' -e 's/$/ i/' $1.angle.pot.new | tac | sed -e '1,0d' |
> tac > $1.angle.cut
>
> source /opt/apps/votca/1.2.3/bin/VOTCARC.bash
> source /opt/apps/gmx/single/463/bin/GMXRC
> csg_call table smooth $1.angle.cut $1.angle.smooth
> csg_resample --in $1.angle.smooth --out $1.angle.refined --grid
> 0::0.001:3.141592654
> csg_call table extrapolate --function quadratic --region left
> $1.angle.refined $1.angle.refined
> csg_call table extrapolate --function linear --region right
> $1.angle.refined $1.angle.refined
> awk '{print $1/3.141592654*180.0,$2}' $1.angle.refined >
> $1.angle.pot.cur
> csg_call --ia-type angle --ia-name $1.angle --options ../convert.xml
> convert_potential gromacs
>
> cd ..
> rm 'done'
> i_c=`expr $i_in + 1`
> sed -i s/iterations_max\>$i_in/iterations_max\>$i_c/ settings.xml
> sh run.sh
> fi
>
> Please share your thought on this.
>
> Chandan
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
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--
Christoph Junghans
Web: http://www.compphys.de
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