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. 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.
