On Thu, Jul 11, 2019 at 9:53 AM Christoph Junghans <[email protected]>
wrote:
>
> On Thu, Jul 11, 2019 at 9:45 AM 徐祥 <[email protected]> wrote:
> >
> > Hi Christoph,
> >
> > Now I can get the topol.xml through a script. But for my test system of
polyamide with 5 monomer, when I use csg_map --top topol.xml --cg pa6.xml
--trj chemistry.dump --out cg-pa6.dump, there was a error:
> >
> > coarse-grained bead is bigger than half the box
> > (atoms 8 (id 46), 17 (id 55) , molecule 1)
> >
> > as I checked in OVITO, these two atoms are not in one bead. Is that
because of periodic boundary condition? I would really appreciate when you
could give me any advices.
>
> If the two atoms aren't in one bead, this error shouldn't occur, so my
> guess is that your mapping file isn't quite correct yet.
Btw, looking at at "csg_dump --top topol.xml",
Atoms with id 46 and id 55 are:
46 Name 1:P:9 Type hc Mass 1.00797 Resnr 0 Resname P Charge 0.053
55 Name 1:P:18 Type hc Mass 1.00797 Resnr 0 Resname P Charge 0.053
and then at
<cg_bead>
<name>A6</name>
<type>A</type>
<mapping>A</mapping>
<beads> 1:P:8 1:P:9 1:P:10 1:P:11 1:P:12 1:P:13 1:P:14 1:P:15
1:P:16 1:P:17 1:P:18 1:P:19 </beads>
</cg_bead>
in pa6.xml, you see that P:9 and P:18 and indeed part of on bead.
The atoms in question had coordinates of [2.33991, 11.0489, 1.08234]
[11.8104, 4.10459, 11.535] (from error message)
with a box length on 12.46, the periodic distance is 6.60238 (=
sqrt((11.535-1.08234-1.2469595330000001e+01)**2+(11.8104-2.33991-1.2469595330000001e+01)**2+(11.0489-4.10459-1.2469595330000001e+01)**2))
and hence bigger than half a box length (6.23).
>
> Christoph
> >
> > Sincerely,
> > Xiang
> >
> > 在 2019年6月27日星期四 UTC+2下午5:19:15，Christoph Junghans写道：
> >>
> >> On Thu, Jun 27, 2019 at 8:23 AM 徐祥 <[email protected]> wrote:
> >> >
> >> > Hi Christoph,
> >> >
> >> > I checked my input file for atomistic simulation and I found that I
have wrote 'fx fy fy' for dump command and now all calculations run well.
Thank you very much for your suggestion.
> >> >
> >> > I have another question about a big PA6 system with around 500 000
atoms. There is only one type molecule which composes of 350 monomers. When
I want use lammps dump file to write out the coarse grained dump file, I
need to manually to redefine every atoms in one molecule in the topol.xml
file. It seems to be a big project.I am wondering, if there is a simpler
method to get topol.xml file. Or can you give me some suggestion about how
to get coarse grained trajectory from lammps dump file?
> >> >
> >> You can use the stock tool, http://stock.cmm.ki.si/smt/, but I usually
> >> write a small script to write the mapping files for bigger molecules.
> >>
> >> Christoph
> >> >
> >> > 在 2019年6月25日星期二 UTC+2下午5:14:32，Christoph Junghans写道：
> >> >>
> >> >> On Tue, Jun 25, 2019 at 7:00 AM 徐祥 <[email protected]> wrote:
> >> >> >
> >> >> > Dear Votca user,
> >> >> >
> >> >> > I want to use csg_map to print out the coarse grained .dump file
and then using force matching with fix mscg in LAMMPS. But something
strange happened in the output file with fz part.
> >> >> > At the same time, I'm not sure whether the force in x and y
direction are correct or not.
> >> >> >
> >> >> > I'd really appriciate when anyone can give me advices on how to
write the force out to coarse grained dump file.
> >> >> Are the cg positions in the right spots? Have you tried to calculate
> >> >> the force by hand for one molecule to check the output?
> >> >>
> >> >> Christoph
> >> >>
> >> >> > Sincerely
> >> >> > Xiang
> >> >> >
> >> >> > Command that I used: csg_map --top topol.xml --trj equil.dump
--cg pa6.xml --force --out cg-pa6.dump
> >> >> >
> >> >> > cg-pa6.dump:
> >> >> > ITEM: TIMESTEP
> >> >> > 0
> >> >> > ITEM: NUMBER OF ATOMS
> >> >> > 14
> >> >> > ITEM: BOX BOUNDS pp pp pp
> >> >> > 0 7.580733
> >> >> > 0 7.580733
> >> >> > 0 7.580733
> >> >> > ITEM: ATOMS id type x y z vx vy vz fx fy fz
> >> >> > 1 0 1.494355 5.404279 2.907944 0.000000 0.000000 0.000000
12.592400 -8.377850
2364558032109094518889807635948683089570290241435415640820108792995599899436389788035156285502740606890601998922988529557877069609479960232025272358933154586821185153955592591638528.000000
> >> >> > 2 1 2.243347 4.295022 4.439319 0.000000 0.000000 0.000000
13.479409 20.502260 0.000000
> >> >> > 3 1 2.189802 5.142636 5.923261 0.000000 0.000000 0.000000
3.866210 -23.597252 0.000000
> >> >> > 4 1 3.512938 6.026377 6.282445 0.000000 0.000000 0.000000
-9.861500 19.987040 0.000000
> >> >> > 5 1 3.926211 7.069904 5.005361 0.000000 0.000000 0.000000
9.756520 -4.570800 0.000000
> >> >> > 6 1 3.486172 0.987056 5.492920 0.000000 0.000000 0.000000
-3.419280 -4.679090 0.000000
> >> >> > 7 2 4.307480 1.466052 6.723431 0.000000 0.000000 0.000000
-2.598060 -8.584390 0.000000
> >> >> > 8 0 5.289278 4.682029 2.350134 0.000000 0.000000 0.000000
-14.249870 19.920390 0.000000
> >> >> > 9 1 5.789601 4.273695 4.227886 0.000000 0.000000 0.000000
17.436400 -18.399210 0.000000
> >> >> > 10 1 6.045801 2.682748 4.436048 0.000000 0.000000 0.000000
-26.629610 23.138802 0.000000
> >> >> > 11 1 7.252864 2.148874 3.534152 0.000000 0.000000 0.000000
18.012220 -4.469040 0.000000
> >> >> > 12 1 0.184249 0.859154 4.367202 0.000000 0.000000 0.000000
24.419730 -7.101160 0.000000
> >> >> > 13 1 0.196048 0.857591 6.080679 0.000000 0.000000 0.000000
-14.616470 15.636000 0.000000
> >> >> > 14 2 0.946176 2.051363 6.933684 0.000000 0.000000 0.000000
-28.187900 -19.405670 0.000000
> >> >> >
> >> >> > --
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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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> --
> Christoph Junghans
> Web: http://www.compphys.de
--
Christoph Junghans
Web: http://www.compphys.de
--
Christoph Junghans
Web: http://www.compphys.de
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