Thanks Christoph, I will tweak the min and max.
Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Sat, Aug 31, 2013 at 10:03 PM, Christoph Junghans <[email protected]>wrote: > 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. > -- 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.
