On Sun, Jun 23, 2019 at 10:35 PM 롤롱이 <[email protected]> wrote: > > Hi, I'm using VOTCA 1.4.1 to develop polymer chain potential in water > > After develop bonded & non bonded potential through IBI, I tested long > simulation with developed potential and the system was exploded after 100ns > (during IBI, I tested only for 10ns, and the explosion occur at various > simulation time other than 100ns) > > The reason, I guess, is the dihedral potential since it has fluctuation in > pot file > > To solve the problem by removing fluctuation, I marked 'o' to the fluctuation > value for purpose of extrapolation. > > and then, I typed the command > csg_call table extrapolate --avgpoints 5 ABAB-dihedral.dist.tgt ABAB.dist.new > > But, the input file (ABAB-dihedral.dist.tgt) is exactly same as output > file(ABAB.dist.new). > > when I used various options --function exponential , --avgpoints with > different value, the result was same > > and also I tested table extrapolate with pot file, ABAB-dihedral.pot.raw. > ,but also it gave me the same result as former. > > It's weird that nothing change > > The manual said, > > [4.2.3] Extrapolation > csg_call table extrapolate [options] table_resample.pot \ > table_extrapolate.pot > > "all values in the potential file that should be used as a basis for > extrapolation > are marked with an i, while all values that need extrapolation are marked by > o. The command > above now extrapolates all o values from the i values in the file." Only the first interval of "i" values get picked up, so you cannot put "o" in the middle of the file.
> > > What should I do to remove fluctuation from the dist or pot file? There is also a smoothing update you could try. > > The fluctuation in potential file could cause the system to be exploded? Maybe, that depends on your system. Christoph > > I attached the ABAB-dihedral.dist.tgt, ABAB-dihedral.dist.extrapolate, > ABAB-dihedral.pot.raw, ABAB-dihedral.pot.extrapolate > > -- > 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 https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/46563cd9-590e-4fe0-9050-13fedd4baf07%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- 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 https://groups.google.com/group/votca. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e5NfE_kiAA-vYO7FkgKNwY26xV13%2BhMUMtniC8RUCPT4A%40mail.gmail.com. For more options, visit https://groups.google.com/d/optout.
