2014-01-28 Jakub Krajniak <[email protected]>: > On Monday, 27 January 2014 04:47:22 UTC+1, Christoph Junghans wrote: >> >> (...) >> >> >> The theory behind Boltzmann inversion assumes a Boltzmann distribution >> >> (NVT). >> >> Which thermostat are you using? For Espresso++ Langevin thermostat >> >> should to the same as stochastic dynamics. >> > >> > >> > Actually I have moved to Gromacs to not complicate too much. When I look >> > on >> > the >> > temperature, it is kept correctly during the simulation (with sd >> > integrator). >> > >> > The strange thing is with rdfs. In the attachment there is a tgt and >> > .new >> > A-A.dist >> > from step_001. The shapes seem similar but the y-values are different. >> > In >> > the next >> > steps the rdfs look totally different (and the .conv value rise >> > enormous). >> 1.) Your target distribution is really noisy, which will lead to a >> very noisy initial potential, maybe a bigger spacing would help. >> 2.) It seems the first update makes the A-A potential too attractive, >> hence you get the really high peak at x=0.42, maybe you will need to >> scale the update with a factor like 0.1 (postupd scale). > > > I am very appreciate for your help. The scale factor helped to remove this > huge difference. I am wondering why I encountered that. Is it possible that > it is because of bond interaction? I have defined the exclusion list for > .top so > this should be handled and the behavior does not changed. This is very system-dependent, in most cases this means your initial potential isn't good enough.
> > Best regards, > Jakub Krajniak > > -- > 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.
