On Tue, Nov 20, 2018 at 6:44 PM Lee <liuchongm...@gmail.com> 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+unsubscr...@googlegroups.com. > To post to this group, send email to votca@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+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
