2015-10-08 3:25 GMT-06:00 Pallavi Banerjee
<[email protected]>:
>
> 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?
That is up to you and the system you are studying! In general any
extrapolation is fine as long as it generates a repulsive force.
Christoph
>
> -Pallavi Banerjee
>
>
> On Wednesday, October 9, 2013 at 10:12:42 PM UTC+5:30, Chandan Choudhury
> wrote:
>>
>> 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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--
Christoph Junghans
Web: http://www.compphys.de
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