Yes, you are right. I missed a important item, pressure correction.
But when I add pressure into the <post_update>, the error occurred
"Pressure correction for lammps is not implemented yet". Does the pressure
correction need to be implemented additionally? And how to implement it?
Thanks
在 2018年12月3日星期一 UTC+8上午10:48:57，Christoph Junghans写道：
>
> On Sun, Dec 2, 2018 at 6:40 PM Lee <[email protected] <javascript:>>
> 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
> >> >>>> >> >> > > --
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> >> >>>> >> >> >
> >> >>>> >> >> >
> >> >>>> >> >> >
> >> >>>> >> >> > --
> >> >>>> >> >> > Christoph Junghans
> >> >>>> >> >> > Web: http://www.compphys.de
> >> >>>> >> >>
> >> >>>> >> >>
> >> >>>> >> >>
> >> >>>> >> >> --
> >> >>>> >> >> Christoph Junghans
> >> >>>> >> >> Web: http://www.compphys.de
> >> >>>> >> >
> >> >>>> >> > --
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> >> >>>> >>
> >> >>>> >>
> >> >>>> >>
> >> >>>> >> --
> >> >>>> >> Christoph Junghans
> >> >>>> >> Web: http://www.compphys.de
> >> >>>> >
> >> >>>> > --
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> >> >>>>
> >> >>>>
> >> >>>>
> >> >>>> --
> >> >>>> Christoph Junghans
> >> >>>> Web: http://www.compphys.de
> >> >>>
> >> >>> --
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> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >
> >> > --
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> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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