2015-11-14 1:49 GMT-07:00 Pallavi Banerjee <[email protected]>: > What confounds me more is if I perform the very same procedure, i.e. > IBI+MARTINI, on a system of single chain of polymer in water, this problem > doesn't show up. On a system of multiple polymer chains in water, the error > sprouts up almost immediately. If there was something wrong with the bond > potential, the system of single chain in water should have crashed as well. Well, looking a the shape of the potential can never hurt. But if the problem only shows up when multiple chain are present you might need to fix the pbc of the initial configuration. Try: $ gmx trjconv -f conf_in.gro -o conf_out.gro -pbc mol
Christoph > > Any insights? > > Many thanks. > > -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.
