2013/7/3 <[email protected]>: > 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 > > 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]. > 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.
