W dniu środa, 3 lipca 2013 15:56:40 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/3 <[email protected] <javascript:>>: > > Dear Users, > > > > I created angular tables using VOTCA. Please, see attached the example. > > When I run gromacs I get LINCS warnings in terms of the constraints > > (distance between beads deviates) and this is related to the angular > tables: > > I checked with other tables and the job is running with no errors. > > May that be the problem of the derivatives in the first (its 0) and the > last > > line (its 0)? How to calculate them? > I don't think the first (0 degrees) and last force (180 degress) > matters, also gromacs will warn you if forces and potential don't fit > together. > In the table there are two big jumps in the potential (around 88 and > 150 degree), you might have to smooth these a bit more as they appear > at 5kJ/mol, which is only 2kT. > > VOTCA automatically extrapolates bonded interaction to the left and > the right from the sampled region exponentially with a derivatives > being of the average of the last 5 points. > That might not be the best choice for all systems! > > Christoph >
Thank you. I sorted it out using exponential extrapolation instead of cubic. Steven > > > > Please, advise/ > > > > Steven > > > > -- > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
