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.
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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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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