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. 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 >> >> > >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, send >> >> > an email to [email protected]. >> >> > To post to this group, send email to [email protected]. >> >> > Visit this group at https://groups.google.com/group/votca. >> >> > To view this discussion on the web visit >> >> > https://groups.google.com/d/msgid/votca/e686097e-e5d2-4ca0-8111-0d844c53553c%40googlegroups.com. >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/48c207bc-6594-4299-80c5-63efed1f5a70%40googlegroups.com. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/e8e79fa7-8297-4318-b3fc-209552eabcf2%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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