Dear Christoph,
Thank you for your response. How do I define exclusion of angle in
mapping file, xml?
"csg_stat" needs two types xml files, one for molecule (DGA.xml) and one
for fmatch.xml.
Where do I define the exclusion of angle or bond during rdf calculation?
The following is a molecule xml mapping file. famtch.xml from tutorials has
no exclusion information.
Thank you.
Best regards,
Changwoon Jang
<cg_molecule>
<name>Other_chain_A</name>
<ident>Other_chain_A</ident>
<topology>
<cg_beads>
<cg_bead>
<name>A1</name>
<type>A</type>
<mapping>A</mapping>
<beads>1:DGA:O 1:DGA:O1 1:DGA:C 1:DGA:C1 1:DGA:C2 1:DGA:C3 1:DGA:C4
1:DGA:C5 1:DGA:C6 1:DGA:C7 1:DGA:C8 1:DGA:H 1:DGA:H1 1:DGA:H2 1:DGA:H3
1:DGA:H4 1:DGA:H5 1:DGA:H6 1:DGA:H7 1:DGA:H8 1:DGA:H9 1:DGA:H10</beads>
</cg_bead>
<cg_bead>
<name>A2</name>
<type>A</type>
<mapping>A</mapping>
<beads>1:DGA:O2 1:DGA:O3 1:DGA:C12 1:DGA:C13 1:DGA:C14 1:DGA:C15
1:DGA:C16 1:DGA:C17 1:DGA:C18 1:DGA:C19 1:DGA:C20 1:DGA:H17 1:DGA:H18
1:DGA:H19 1:DGA:H20 1:DGA:H21 1:DGA:H22 1:DGA:H23 1:DGA:H24 1:DGA:H25
1:DGA:H26 1:DGA:H27</beads>
</cg_bead>
<cg_bead>
<name>B1</name>
<type>B</type>
<mapping>B</mapping>
<beads>1:DGA:C9 1:DGA:C10 1:DGA:C11 1:DGA:H11 1:DGA:H12 1:DGA:H13
1:DGA:H14 1:DGA:H15 1:DGA:H16</beads>
</cg_bead>
</cg_beads>
<cg_bonded>
<bond>
<name>bond</name>
<beads>
A1 B1
A2 B1
</beads>
</bond>
<angle>
<name>angle</name>
<beads>
A1 B1 A2
</beads>
</angle>
</cg_bonded>
</topology>
<maps>
<map>
<name>A</name>
<weights>16 16 12 12 12 12 12 12 12 12 12 1 1 1 1 1 1 1 1 1 1
1</weights>
</map>
<map>
<name>B</name>
<weights>12 12 12 1 1 1 1 1 1</weights>
</map>
</maps>
</cg_molecule>
On Tue, Jun 28, 2016 at 10:00 AM, Christoph Junghans <[email protected]>
wrote:
> 2016-06-27 15:33 GMT-06:00 Chang Woon Jang <[email protected]>:
> > 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?
> If the exclusion list says they are not excluded, so be it. You can
> add an angle between A-B-C (or a bond between A-C) in the mapping file
> to exclude them in rdf calculation.
>
> Christoph
>
> >
> > 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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> >>> >> > "votca" group.
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> >>> >> > 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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> >>> >
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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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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
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