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.
