Thanks for the suggestion, Christoph. It worked. Chandan
-- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jan 1, 2014 at 5:53 AM, Christoph Junghans <[email protected]>wrote: > 2013/12/31 Chandan Choudhury <[email protected]>: > > 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. > That happened to me, too. To check my mapping file, I usually map one > configuration using csg_map. > And then visualize the atomistic and coarse-grained snapshot using vmd > to see if they sit on top of each other. > > Cheers, > > Christoph > > > > 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. > > > > -- > 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.
