2015-11-13 1:59 GMT-07:00 Pallavi Banerjee <[email protected]>: > Yeah, you're right. Including the MARTINI L-J parameters directly would make > more sense. > > But on doing this, I get the following error message: > > A tabulated bond interaction table number 1 is out of the table range: r > 2.510421, between table indices 1255 and 1256, table length 1251 That basically means something is wrong with the 1st bond table (table_b1.xvg). Usually the end of the bonded interactions has not been extrapolated enough. For big r the table should increase steeply. In general the potential for bond should look like a deformed letter U.
> This doesn't happen when I do pure IBI on the whole system. Any help > regarding circumventing this would be much appreciated. > > And regarding the 4:1 mapping with IBI would require greater effort since > the k-clustering algorithm would have to be implemented, which is further > down the line if this approach doesn't work out. > > > 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.
