In votca, the smoothing process works for potential. Is there any smoothing process for new distribution? And what's the command?
在 2018年11月21日星期三 UTC+8下午9:03:19，Christoph Junghans写道： > > On Tue, Nov 20, 2018 at 6:44 PM Lee <liucho...@gmail.com <javascript:>> > wrote: > > > > The expression of boltzmann inversion is V=-kBTln(P). And the > distribution P is related to the scale of the x-coordinate. The plot of > bond distribution with different units are attached. In votca, all the > processes including calculating distributions and boltzmann inversion are > finished with units nm. So can I say that the obtained potential table used > in lammps is converted by V=-kBTln(P) with the length units nm? So in > lammps, the dynamic simulation is finished with length units angstroms but > with the potential corresponding to units nm. > > Well, V(x)= -kBTln(P(x)) and x can be a distance or an angle etc. V > and P are always parameterized by the same variable in its units. Also > P(x) is a distribution and hence is unit-less, plus the normalization > of the distribution doesn't matter much as ln(a*P)=ln a + ln P and > hence only leads to an irrelevant offset in the potential and doesn't > matter to the forces. > > Christoph > > > > > 在 2018年11月20日星期二 UTC+8下午11:43:59，Christoph Junghans写道： > >> > >> On Tue, Nov 20, 2018 at 2:04 AM Lee <liucho...@gmail.com> wrote: > >> > > >> > I have another question. If my units command is real in lammps > which the units of distance and energy are angstroms and Kcal/mole > respectively, what shoud I change in the setting file in order to get the > potential table with right units? Now, the bond and angle potential of the > CG system are much lower than the corresponding atomic system. > >> > >> Usually VOTCA calculated things in Gromacs units (so nm, kJ/mol etc.), > >> but if you only calculate RDFs you don't need to change anything as > >> input and output are both in nm and hence there is no scaling > >> involved. So this will work for angstroms as well. Additionally, you > >> need to make sure that kBT is in the right unit in the settings file. > >> > >> Christoph > >> > Thanks a lot. > >> > > >> > 在 2018年11月20日星期二 UTC+8上午5:52:29，Christoph Junghans写道： > >> >> > >> >> On Mon, Nov 19, 2018 at 8:51 AM Christoph Junghans < > jung...@votca.org> wrote: > >> >> > > >> >> > On Sun, Nov 18, 2018 at 8:31 PM Lee <liucho...@gmail.com> wrote: > >> >> > > > >> >> > > For the dynamic simulations finished with lammps, should I set > the exclusions? If excluding non-bonded interactions between atoms that are > no further than 3 bonds away, does it need to excluding these atoms when > statistical target rdf distributon? > >> >> > > > >> >> > Yes, for LAMMPS you will most likely need to create rdf exclusion > manually. > >> >> > > >> >> > You can check, what exclusion VOTCA see by running: > >> >> > $ csg_dump --top <your_topology_file> --excl > >> >> > > >> >> > For advanced topology handling see, section 3.3 of the manual, > >> >> > http://doc.votca.org/manual.pdf > >> >> Also Joshua might be able to say something about the new LAMMPS > >> >> topology reader in csg and how exclusions are incorporated there. > >> >> > >> >> Christoph > >> >> > > >> >> > Christoph > >> >> > > -- > >> >> > > 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 votca+un...@googlegroups.com. > >> >> > > To post to this group, send email to vo...@googlegroups.com. > >> >> > > Visit this group at https://groups.google.com/group/votca. > >> >> > > For more options, visit https://groups.google.com/d/optout. > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Christoph Junghans > >> >> > Web: http://www.compphys.de > >> >> > >> >> > >> >> > >> >> -- > >> >> 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 votca+un...@googlegroups.com. > >> > To post to this group, send email to vo...@googlegroups.com. > >> > Visit this group at https://groups.google.com/group/votca. > >> > 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 votca+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > 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. 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