On Sun, Dec 2, 2018 at 6:40 PM Lee <[email protected]> wrote: > > By checking the convergence value of interaction, I found that it was > stabilized above 1. When I use these potential table to do the cg simulation, > the density of cg system is half of that the corresponding atomic system. So > I think the nonbond interaction is still immature. How to reach a lower > convergence number? The rdf and the convergence number of C-C are attched.
Run longer iterations, finer binsize, in general everything which increases the statistics helps. On the other hand, your RDF conversion looks pretty good already, don't let this one number guide you, you need to test the coarse-grained model, too. Christoph > > 在 2018年12月1日星期六 UTC+8下午9:44:34，Christoph Junghans写道： >> >> On Fri, Nov 30, 2018 at 8:00 PM Lee <[email protected]> wrote: >> > >> > OK, thanks! I have increased the bin size and the distribution seems >> > to be smoothed. >> > In some paper, the IBI process is started from bond and then angle, >> > the nonbonded potential is finished at last. When doing ibi for bond and >> > angle, the pair interaction is turned off. The chains are pushed apart to >> > remove close contacts by slowly turning on a soft, purely repulsive >> > potential as you said before. But I couldn't find the command in lammps. >> That might be a question for the lammps mailing list! >> >> > Another question, how could I output the value of convergence for >> > every iterative step? >> The convergence numbers are stores in a files for each interaction >> called <NAME>.conv and the sum is printed in the log files, so you can >> do: >> $ grep "Convergence sum" inverse.log >> >> This of course assumes you enabled the convergence check feature (with >> setting cg.inverse.convergence_check.type to "default") >> >> Christoph >> > >> > 在 2018年11月30日星期五 UTC+8下午11:24:33，Christoph Junghans写道： >> >> >> >> >> >> >> >> 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. >> >> >> >> -- >> 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. 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