2013/12/30 Chandan Choudhury <[email protected]>: > Dear votca users, > > I am iterating the bonded part of the polymer (with following sequence: > A1-B1-C1-B2-D1-B3-C2-B4-D2-B5-C3-E1). > > I am generating bond distribution using the csg_boltzmann utility. > The mapping file contains the bonds, angles and dihedrals information. > > When I try to generate the bond distributions for the beads consisting of > additional bonds (1-4) and angles. The distributions obtained doesnot > matches with the one generated by not including the extra bonds & angles. > > I have attached both the mapping files. map.xml consists the information > about the additions bonds & angle while map1.xml do not contain these. > > command used: > cat csg_boltzmann.txt | csg_boltzmann --trj 70-91_PC-trimer_whole.xtc --top > mdtrim510K_41-91ns.tpr --cg map1.xml > > & > cat csg_boltzmann.txt | csg_boltzmann --trj 70-91_PC-trimer_whole.xtc --top > mdtrim510K_41-91ns.tpr --cg map.xml > > The BD_map.bond and BC_map.bond are obtained using the map.xml (containing > the additional bond information) file. When looking at the difference between map.xml and map1.xml $ diff -w map.xml map1.xml | less I saw that the order of 1:mma:CA1 and 1:mma:H4 in the definition of B2 (2:mma:CA1/H4 in B4) is inverted, in combination with the order of the weights in mapping "B" this will lead to a weight of 12 for H4 and a weight of 1 for CA1 and that might be the reason for these odd distributions.
Cheers, Christoph > > This behavior is only shown for BC & BD beads. For my case I donot see any > significant effect in the angle distributions. > The BC.bond and BD.bond matches with the distributions generated from > myself. > > Why is this happening? What am I missing? Any guidance would be very > helpful. > > 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/groups/opt_out. -- 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/groups/opt_out.
