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.
