Dear Massimo, the potentials indeed looks a bit funny. I'm currently running the tutorial to verify everything is correct in there. Will get back to you later.
As a general remark, very different potentials can lead to almost identical RDFs. When we did the simulations, the RDF looked great after 5-10 iterations, but then it took another ~200 to get to its final shape. Victor 2012/9/25 massimo sandal <[email protected]>: > Hi, > > To learn VOTCA, I am trying to reproduce the water potential as in the > original VOTCA paper, using IBI (Ruhle et al., J. Chem. Theory Comput., > Vol. 5, No. 12, 2009 , fig. 2A). Unfortunately it seems that I can't. The > RDF converges very quickly and very well, but the potential is completely > different from the one of the paper. This happens even with the tutorial > files (v. 1.2.2) > > See here for an example of what I mean: http://imgur.com/a/c74Yw > > I am using Gromacs 4.5.5 single precision. The only difference in the > settings file from the tutorial is where I specify the name of the binaries. > The settings.xml is attached. The trajectories at each step seem healthy, > visually. > > What can I do to troubleshoot this? > > Thanks, > Massimo > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/votca/-/BmWtWnAu8lQJ. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
