On Fri, Nov 30, 2018 at 01:05 Lee <[email protected]> wrote: > In votca, the smoothing process works for potential. Is there any > smoothing process for new distribution? And what's the command? > No, but it would be hard to add!
Also increasing the bin size naturally does smoothing! Christoph > > > 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 <[email protected]> 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 <[email protected]> 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]. >> >> > 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 >> > >> > -- >> > 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 >> > -- > 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 -- 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.
