Thanks for reply! 2019년 6월 26일 수요일 오전 12시 9분 10초 UTC+9, Christoph Junghans 님의 말: > > On Sun, Jun 23, 2019 at 10:35 PM 롤롱이 <[email protected] <javascript:>> > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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