2013/8/30 Chandan Choudhury <[email protected]> > > Dear votca users, > > I have a small clarifications regarding the tabulated potentials (bonded) > generated by votca (1.3-dev). > > The distributions are converted to potentials and the refined and > extrapolated and then converted to the tabulated potentials. In 1.2.3, these > processes were manually done. > > For a spring potential, one would expect the rise in potential for 'r' away > from minima and this should also be reflected in the tabulated potentials. > > I have attached the bonded distribution and its tab. potentials for step_001, > what I find is that the tab. potential saturates at large r. > > I have also attached one of the angle distributions (points exceeding > 1.1056700000e+02 has been deleted as the value were exactly same. This also > reduced the file size below 8.0 MB). This angle also shows the spring > behavior. The similar observation is observed. > > Is the above behavior normal for spring-type potentials. > > > One more relating to this I could not understand was, when I input a spring > potential in the topology file, the bond fluctuates around the r_minimum. > But, when I generate the tabulated potential out of the same potential, and > now I input this tab. potential, the bond distributions are nowhere near to > the r_min. Is this normal or something I am missing. Any insight would be of > great help.
I had a look at your files and I think I know where your problem are coming from! When Votca does an extrapolation of the potential in the process of converting *.pot.cur into *.xvg, it calculated the derivative from the last point on each side.In your BDB.angle.pot.cur the first two point are equal and hence the extrapolation fails. I will have to think a bit on how to improve this magic, but for now the easiest would be to increase min and decrease max, so that the distribution is still bigger 0 for min and max and allow a better estimation of the derivative of the potential. Christoph > > Chandan > > -- > 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.
