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.
