Dear Christoph,
In the settings.xml file what should be the value of cg. inverse. kBT, if
am using LAMMPS (real units) as a simulation program as shown below:
<inverse>
<kBT>2.49435</kBT>
</simulation>
<program>lammps</program>
<!-- lammps specific options -->
If my T = 300 K, should it be *300 ** *0.00198720 = 0.5962 kcal/mol K, or
300 * 0.0083144621* = *2.49434 kJ/mol K.*
Thank you.
Sanjeet
On Tuesday, November 8, 2022 at 2:59:36 PM UTC-5 Christoph Junghans wrote:
> On Tue, Nov 8, 2022 at 12:05 PM Sanjeet Singh <[email protected]> wrote:
> >
> > Hello Christoph,
> >
> > I applied all your suggestions and replaced the tabulated bond
> stretching potential with the harmonic functional form. And now I am
> getting somewhat improved result.
> Good, I always recommend doing non-bonded only first and then throwing
> the bonded interactions later.
>
> >
> > But, again convergence problem is there. Furthermore, at some steps of
> the iterations, I found that two beads of my system are in direct contact
> with each other.
> >
> > Can you please point out the reason for this, and the possible remedy?
> That is a very system specific question. But I guess you will have to
> increase the repulsive core of the non-bonded interactions.Check the
> file <name>.pot (or whatever name you picked in the settings file) in
> the last step_* directory to see if it is extrapolated/repulsive
> enough.
> Usually you can do that by increasing the repulsive core by increasing
> the <min> of said interaction a bit.
>
> Christoph
> >
> > I am also attaching snapshots of the simulation box for your reference.
> >
> > Thank you.
> >
> > Sanjeet
> >
> > On Monday, November 7, 2022 at 9:34:22 AM UTC-5 Christoph Junghans wrote:
> >>
> >> On Sun, Nov 6, 2022 at 6:47 PM Sanjeet Singh <[email protected]>
> wrote:
> >> >
> >> > Hello Christoph,
> >> >
> >> > I am trying to perform IBI for non-bonded interaction. I have 3 bead
> types in my system.
> >> >
> >> > I have already run it for more than 500 iterations, but IBI is not
> able to reproduce the target distribution.
> >> >
> >> > Can you please suggest on how to work on this?
> >> I look like you don't have enough statistics in each iteration, you
> >> could do the following:
> >> - more MD steps
> >> - decrease the step size - 0.002 seems a bit too small
> >> - using scale and potential_do will also throw out some of the stats.
> >>
> >> Regarding the peak around 0.35nm in the Bead2-Bead2 plot, it seems to
> >> me you count an intra-moleculde pair there.
> >> If that is the case, you will need to exclude that.
> >> You can search the mailing for more details, but in short, just add a
> >> bond section in your topology.xml (see
> >>
> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/atomistic/hexane.xml#L26
> )
> >> and use said topology file instead of the data file.
> >> Inttra molecular interaction will automatically generate exclusion,
> >> you can check that with: csg_dump --top topology.xml --excl
> >>
> >> Christoph
> >>
> >> >
> >> > I am hereby attaching the rdf for two of the non-bonded interactions
> in my system along with the setting.xml file.
> >> >
> >> > Thank you.
> >> >
> >> > Sanjeet
> >> >
> >> >
> >> > --
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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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