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:
For the first iteration, I used the tabulated potentials generated from the
csg_boltzmann. Upon its completion, I used the following scripts:
*#!/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\>$i_c/ settings.xml
sh run.sh
fi*
The *i_in* is the variable which is the iteration step.
These commands generate tabulated potentials for the bond type. Then this
tabulated potential is the input for the next iteration. (What I did was I
stopped the the iteration with the simulation by gromacs starts. Then copy
the tabulated potential for the earlier step and again execute run.sh)
The above script comes into picture if there is bad sampled region in the
new potential. The bad sampled region is manually identified and the values
goes as an input in the sed command. The region is cut and then other
commands follow. I use 1.2.3 for this purpose and 1.3-dev gets sourced in
the run.sh.
Here, I iterated one bond and then 2nd and so on.
The same procedure is followed for generating optimized potentials for
angles.
*#!/bin/sh
i_in=3
if [ "$#" -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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