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. 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 -- 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.
