On Tue, Dec 31, 2013 at 12:12 AM, Christoph Junghans <[email protected]>wrote:
> 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. > > Thanks Christoph. On changing the order, the distributions are now consistent. Chandan > 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. > -- 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.
