Dear Christoph,
I am correcting the previous question.
Thank you for the clarification of the list. I have another question. A
molecule is bonded with A-B-C beads. The first bead (A) is mapped with
atoms from 1 to 22 and the second bead (B) is mapped with atoms from 23 to
31, and the third bead (C) is mapped with 32 to 53. In this exclusion
lists, the first bead (A) and third bead (C) seem to interact each other.
It look like that the atoms in A bead are *fairly (not fully)* interacted
with the atoms in C bead. Therefore, A-C radial distribution function seems
to include 1-3 (A-C) interactions somewhat. Is this correct?
Thank you.
Best regards,
Changwoon Jang
On Mon, Jun 27, 2016 at 5:24 PM, Chang Woon Jang <[email protected]>
wrote:
> Dear Christoph,
>
> Thank you for the clarification of the list. I have another question. A
> molecule is bonded with A-B-C beads. The first bead (A) is mapped with
> atoms from 1 to 22 and the second bead (B) is mapped with atoms from 23 to
> 31, and the third bead (C) is mapped with 32 to 53. In this exclusion
> lists, the first bead (A) and third bead (C) seem to interact each other.
> It look like that the atoms in A bead are fully interacted with the atoms
> in C bead. Therefore, A-C radial distribution function seems to include 1-3
> (A-C) interactions. Is this correct?
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Mon, Jun 27, 2016 at 5:03 PM, Christoph Junghans <[email protected]>
> wrote:
>
>> 2016-06-27 13:37 GMT-06:00 Chang Woon Jang <[email protected]>:
>> > Dear Christoph,
>> >
>> >
>> > I tested the following command.
>> >
>> > csg_dump --top topol.tpr --excl > exclusion_list
>> >
>> > In the exclusion_list file, the number are listed like
>> >
>> > I have 15000 beads in 300 molecules
>> >
>> > List of exclusions:
>> > 1 2 3 4 5 6 7 8 9 10 11 12
>> > 2 3 4 5 6 7 9
>> > 3 4 5 6 7 9
>> > 4 5 6 7 9
>> > 5 6 7 8 9 10 11 12 13
>> > 6 7 8 9 10 11 12
>> > 7 8 9 10 11 12
>> > 8 9
>> > 9 10 11 12 13 14 21
>> > 10 11 12 13
>> > 11 12 13
>> > 12 13 14 15 16 19 21 22
>> > 13 14 15 16 17 19 20 21 22
>> > 18 13 14 15 16 17 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 40
>> > ...
>> >
>> >
>> > What do these numbers mean? The first line has 1 2 3 4 5 6 7 8 9 10 11
>> 12. I
>> > do not know what this series of numbers.
>> It means, atom #1 is exclude with 2, 3, 4, ...
>>
>> >
>> > However, it seems that csg_stat excluded the pairs of beads directly
>> bonded.
>> > Therefore, I do not need consider the 1-3 interactions in CG system in
>> > lammps.
>> >
>> >
>> > I am not sure why the density is higher than atomistic reference density
>> > when I do not apply 1-3 interactions. I have driven tabulated potential
>> > using ibi pressure correction method. Are there any suggestions for
>> better
>> > CG simulation to fix the density?
>> >
>> > Thank you.
>> >
>> > Best regards,
>> > Changwoon Jang
>> >
>> >
>> >
>> > On Mon, Jun 27, 2016 at 3:15 PM, Christoph Junghans <[email protected]
>> >
>> > wrote:
>> >>
>> >> 2016-06-27 12:58 GMT-06:00 Chang Woon Jang <[email protected]>:
>> >> > Dear VOTCA users,
>> >> >
>> >> > I have a question about radial distribution functions from
>> csg_stat.
>> >> >
>> >> > I have obtained radial distribution functions and used them for
>> >> > iterative
>> >> > boltzmann inversion to derive non-bonded tabulated potentials. After
>> >> > some
>> >> > iterations, the calculated radial distribution functions were well
>> >> > matched
>> >> > with reference RDF from csg_stat. Then, I used the obtained tabulated
>> >> > potentials for lammps simulations.
>> >> >
>> >> > From the lammps simulation with tabulated potentials, the liquid
>> >> > polymer
>> >> > system has higher density (1.3 g/cc) than the experimental density
>> (1.07
>> >> > g/cc) when I do not consider 1-3 bead pairs which are those
>> separated by
>> >> > 3
>> >> > bonds. However, when I applied 1-3 interactions, the simulational
>> >> > density is
>> >> > in good agreement with experimental density.
>> >> >
>> >> > I think that the reference radial distribution functions from
>> >> > csg_stat
>> >> > are calculated with pairs of beads directly bonded to each other as
>> well
>> >> > as
>> >> > non-bonded pairs.
>> >> >
>> >> > Is this correct?
>> >> This depends on your topology file. csg_stat excludes bonds and angles
>> >> automatically.
>> >> However, if you have a topology file without bonds and angles, they
>> >> wont' be excluded.
>> >> To check use:
>> >> $ csg_dump --top topol.xml --excl
>> >>
>> >> Christoph
>> >> >
>> >> > Thank you.
>> >> >
>> >> > Best regards,
>> >> > Changwoon Jang
>> >> >
>> >> >
>> >> > --
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>> >> > email to [email protected].
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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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>>
>
>
>
> --
> Best regards,
> Changwoon Jang,
>
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: [email protected]
>
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