Dear Christoph, Thanks for fixing the bug. I made the changes in the source code and re-installed votca (1.3-dev).
The thing which has been troubling very much is the bonded distributions of AB and DB. The sequence of the polymer is A-B1-C1-D1-B2-C2-D2-B3-E. The other distributions (BC, CD and BE) shows the same behaviour as from the g_rdf (nrexcl=0) command. Infact, on using the csg_boltzmann on the trajectory of step_001, I obtain a well behaved distributions fo all the bond distributions. Infact plots are overlapping for BC, CD and BE (when compared with csg_stat). I donot understand why only these to bonds are behaving in a different way. I have attached the output of AB and DB bonds. AB contains -nan-. One way to get rid of it, I suppose would be to use csg_boltzmann tool. Can it be used for bonded part? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Aug 14, 2013 at 3:34 AM, Christoph Junghans <[email protected]>wrote: > 2013/8/13 Christoph Junghans <[email protected]>: > > 2013/8/13 Chandan Choudhury <[email protected]>: > >> > >> Dear users, > >> > >> I am using votca version 1.3-dev for cg simulation. > >> At step_001, after the simulation by gromacs, csg_stat runs and it > computes > >> the distributions (reads the setting.xml and mapping_cg.xml). > >> > >> My system and 5 different beads with 5 bond and 5 angles. > >> > >> While surprisingly, csg_stat produces incorrect distributions for the > >> AB.bond and DB.bond (xvg attached). > >> As a cross check, I executed the same csg_stat command on the cg > trajectory, > >> which was generated from atomistic simulations (with same setting amd > >> mapping files). The command executes and the plots are reasonable. > >> So, the mapping and setting files are correct. > >> > >> Also, I have used the g_rdf (with exclusion 0), to compute the bond > >> distributions. The distributions for BC, CD and BE matches while for AB > and > >> DB bonds, it didnot match. I cannot undestand where I am mistaken. > Kindly > >> suggest me. > > The bonded ibi feature in new in votca 1.3, it might not be very well > tested. > > > > I have the suspicion that the normalization for the bonded interaction > > might be inconsistent in csg_stat. > > Usually that has no effect on IBI as the only thing, which matters is > > the ratio, so it will works as long as the target distribution has the > > same normalization. > > > > I will have a look into it soon. > Actually, there was a bug! I fixed it: > < > https://code.google.com/p/votca/source/detail?r=ea8e40fb78693ba6fe2dd1d544aff6d6e111b845&repo=csg > > > and also updated the tutorials: > < > https://code.google.com/p/votca/source/detail?r=6e0f1991ad31eda3a86e660637f156a514f217a1&repo=csg-tutorials > > > > I didn't added the factor 1/r , 1/sin at this point, but for IBI that > didn't matter much as long as the target distribution is generated > with csg_stat, too. > > Christoph > > > > For all the other readers, bonded distribution in csg_boltzmann are > > correct and non-bonded distribution in csg_stat, too. The thing in > > question are bonded distribution from csg_stat! > > > >> > >> N.B: I have also attached the settings and mapping files. > >> -- > >> 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 > > > > -- > 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.
AB.bond.dist.new
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DB.bond.dist.new
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