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.
#! /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 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.
