Hello!
I found this post of yours very useful. Could you provide the rationale
behind using linear extrapolation for the angles? Shouldn't they be
quadratic as well?
-Pallavi Banerjee
On Wednesday, October 9, 2013 at 10:12:42 PM UTC+5:30, Chandan Choudhury
wrote:
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> Dear votca users,
>
> I would like to share my experience regarding the iteration of bonded
> interactions.
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> I prefer to use the following script for iterating the bonds:
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> For the first iteration, I used the tabulated potentials generated from
> the csg_boltzmann. Upon its completion, I used the following scripts:
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> *#!/bin/sh i_in=1 if [ "$#" -ne 0 ]; then echo $# cd
> step_00$i_in echo `pwd` 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 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 csg_call table extrapolate --function quadratic
> $1.bond.refined $1.bond.pot.cur 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\>$i_c/ settings.xml sh run.sh
> fi*
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> The *i_in* is the variable which is the iteration step.
> These commands generate tabulated potentials for the bond type. Then this
> tabulated potential is the input for the next iteration. (What I did was I
> stopped the the iteration with the simulation by gromacs starts. Then copy
> the tabulated potential for the earlier step and again execute run.sh)
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> The above script comes into picture if there is bad sampled region in the
> new potential. The bad sampled region is manually identified and the values
> goes as an input in the sed command. The region is cut and then other
> commands follow. I use 1.2.3 for this purpose and 1.3-dev gets sourced in
> the run.sh.
> Here, I iterated one bond and then 2nd and so on.
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> The same procedure is followed for generating optimized potentials for
> angles.
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> *#!/bin/sh i_in=3 if [ "$#" -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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