2015-11-11 2:38 GMT-07:00 Pallavi Banerjee <[email protected]>: > Thanks, Christoph! > > I run the following script to prepare potentials for input to VOTCA. It > would be a great help if you go through this once and see if things make > sense. Here 'W_W' stands for Martini W_W interaction. The input > (W_W.dist.tgt) is the rdf obtained from a separate MARTINI water run. One technical comment below, but in general I am not sure what you are doing. You want to do IBI on the polymer-polymer interaction, but keep the W_W interaction fixed, right? Do why do you need to Boltzmann invert the W_W interaction in the first place? Would it be more useful to simply use the parameter from the MARTINI force field for the W_W interaction?
Christoph > > > > #! /bin/bash > > str='W_W' > > csg_resample --in $str.dist.tgt --out $str.dist.resample --grid 0:0.01:1.5 > > csg_call table extrapolate --function linear --avgpoints 1 --region left > $str.dist.resample $str.dist.extrapolate.left > csg_call table extrapolate --function constant --avgpoints 1 --region right > $str.dist.extrapolate.left $str.dist.extrapolate.final > > ./dist_adjust.pl $str.dist.extrapolate.final $str.dist.shift > > ./dist_boltzmann_invert.pl --type non-bonded --kbT 2.49435 --min 1e-10 > $str.dist.shift $str.raw.pot You could use $csg_call prepare_single ibi ... instead, but otherwise looks fine. > > csg_call --ia-type non-bonded --ia-name $str --options table.xml > convert_potential gromacs $str.raw.pot table_$str.xvg > > > Thanks a lot! > > -Pallavi Banerjee > > > On Tuesday, November 10, 2015 at 8:24:18 PM UTC+5:30, Pallavi Banerjee > wrote: >> >> Hello, >> >> I am trying out this new method of integrating MARTINI and IBI. This is >> because mine is an aqueous system and MARTINI water follows a 4:1 mapping as >> opposed to IBI which limits you to a 1:1 mapping for water. The idea is to >> perform IBI on just polymer-polymer interactions while keeping the potential >> of interactions of water-water and polymer-water fixed. I obtain these >> aforementioned potentials from rdfs of separate MARTINI runs, which I plan >> to provide as input. I am unable to figure out a way to instruct VOTCA to >> take these potentials as they are. >> >> Any help is appreciated. >> >> -Pallavi Banerjee > > -- > 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 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.
