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.
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 <[email protected] <javascript:>> > 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 <[email protected]> > wrote: > >> > > >> > On Sun, Nov 18, 2018 at 8:31 PM Lee <[email protected]> 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 [email protected]. > >> > > To post to this group, send email to [email protected]. > >> > > 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 [email protected] <javascript:>. > > To post to this group, send email to [email protected] > <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. 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. For more options, visit https://groups.google.com/d/optout.
