Thanks. Christoph! Are the only available functions linear and quadratic? -Pallavi Banerjee
On Thu, Oct 8, 2015 at 3:15 PM, Christoph Junghans <[email protected]> wrote: > 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 > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to a topic in the > Google Groups "votca" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/votca/QdlpbKsBdII/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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