I have fitted the distribution by Gaussian curve (the red line) and
use it as the target distribution. But the converted potential presents not
a harmonic form (as shown in ACF.pot.cur.png). I want to know what causes
the potential curve drops sharply at the boundary PI.
And I don't konw what's the meaning of "use an angle type 1 (or 6) in
the gromacs topology for that angle interaction". The MD simulation is
performed by lammps. In my topology, this angle type is already defined.
在 2018年12月19日星期三 UTC+8上午12:01:14，Christoph Junghans写道：
>
> On Tue, Dec 18, 2018 at 6:14 AM Lee <[email protected] <javascript:>>
> wrote:
> >
> > Hi Christoph,
> > Now I want to fit the target distribution with single peak
> gaussian distribution. So the angle potential can be expressed with
> harmonic potential (quadratic form). But if the peak of angle distribution
> close to PI, the target distribution must be truncated at the boundary (PI)
> with a big probability density value (as shown in the figure attched). The
> angle potential converted from this target potential doesn't show a
> harmonic shape. The right part of potential close to PI drops sharply to
> zero. Theoretically, it should present as standard quadratic form just like
> the left half part. So I doubt whether the truncation is the reason because
> the left part without truncated by boundary is perfect.
> > How can I get a standard harmonic potential in this situation? Or
> maybe it's impossible.
>
> Just fit the distribution by hand and use an angle type 1 (or 6) in
> the gromacs topology for that angle interaction.
>
> Christoph
>
> > Thanks very much
> >
> > 在 2018年12月7日星期五 UTC+8下午8:56:34，Christoph Junghans写道：
> >>
> >> On Fri, Dec 7, 2018 at 4:54 AM Lee <[email protected]> wrote:
> >> >
> >> > After I added the pressure correction, the density of the cg system
> is very close to the full-atomic system. Thanks for your advise. But when I
> use these final potential table to do the tensile simulation for cg system,
> the system is unstable. And the stress-strain curve is extrmely terrible. I
> saw someone abtained a good stress-strain curve at
> https://groups.google.com/forum/#!msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ . So
> I want to know how could I get a good stress-strain curve with these
> potential table? Or there still need some post process for these table?
> >>
> >> That is magic of coarse-graining, if you parameterize a model on RDF
> >> and pressure, it isn't obvious that the model will reproduce the
> >> stress-strain curve. Maybe Frank knows some details and can comment
> >> here.
> >>
> >> Christoph
> >> >
> >> > 在 2018年12月3日星期一 UTC+8下午10:58:40，Christoph Junghans写道：
> >> >>
> >> >> On Mon, Dec 3, 2018 at 3:51 AM Lee <[email protected]> wrote:
> >> >> >
> >> >> > 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?
> >> >>
> >> >> Well it just means we haven't added support for pressure correction
> >> >> when using lammps in that version.
> >> >> However, it has been added here
> https://github.com/votca/csg/pull/201,
> >> >> so either patch that in or use the development version of votca
> >> >> instead (see
> https://github.com/votca/votca/blob/master/share/doc/INSTALL.md#general-source-installation-instructions.)
>
>
> >> >>
> >> >> Christoph
> >> >>
> >> >> > 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]> 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
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> >> >> >> >> >>>> >> > 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
> >> >> >> >> >>>> >
> >> >> >> >> >>>> > --
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> >> >> >> >> >>>> > For more options, visit
> https://groups.google.com/d/optout.
> >> >> >> >> >>>>
> >> >> >> >> >>>>
> >> >> >> >> >>>>
> >> >> >> >> >>>> --
> >> >> >> >> >>>> Christoph Junghans
> >> >> >> >> >>>> Web: http://www.compphys.de
> >> >> >> >> >>>
> >> >> >> >> >>> --
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>
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>
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> Christoph Junghans
> >> >> >> >> >> Web: http://www.compphys.de
> >> >> >> >> >
> >> >> >> >> > --
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> 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
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> >> >> >> > To post to this group, send email to [email protected].
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> >> >> >> > 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].
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> >> >> > 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].
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> >> > For more options, visit https://groups.google.com/d/optout.
> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
> > --
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>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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