Furthermore, where is the resname DUM coming from? On Monday, February 21, 2022 at 4:54:43 PM UTC-5 Satyen Dhamankar wrote:
> Oh sorry for the misunderstanding. I have already run a SPCE simulation in > LAMMPS. I wanted to get the coarse-grained initial config using csg_map, > however, i am not sure how to go about making the mapping.xml file using > the current directions that you have. > > This is what I see when I run csg_dump --top sys.data, this is what I see: > ``` > WARNING: The votca lammps data reader is only able to read lammps files > formatted in the following styles: > angle > atom > bond > full > molecule > > These styles use the following formats in the atom block: > atom-ID molecule-ID atom-type charge x y z > atom-ID molecule-ID atom-type charge x y z nx ny nz > atom-ID molecule-ID atom-type x y z > atom-ID molecule-ID atom-type x y z nx ny nz > atom-ID atom-type x y z > atom-ID atom-type x y z nx ny nz > > I have 2187 beads in 729 molecules > Boundary Condition: orthorhombic > Box matix: 2.8 0 0 > 0 2.8 0 > 0 0 2.8 > > List of residues: > 0 name: DUM id: 0 > 1 name: DUM id: 1 > 2 name: DUM id: 2 > 3 name: DUM id: 3 > 4 name: DUM id: 4 > 5 name: DUM id: 5 > 6 name: DUM id: 6 > 7 name: DUM id: 7 > 8 name: DUM id: 8 > 9 name: DUM id: 9 > ... > List of molecules: > molecule: 1 H2O1 beads: 3 > 0 Name O1 Type O1 Mass 15.9994 Resnr 0 Resname DUM Charge -0.82 > 1 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41 > 2 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41 > molecule: 2 H2O1 beads: 3 > 3 Name O1 Type O1 Mass 15.9994 Resnr 1 Resname DUM Charge -0.82 > 4 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41 > 5 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41 > molecule: 3 H2O1 beads: 3 > ... > ``` > Reading the above, molecule name is H2O1. What I dont get, is that the H2 > molecules are exactly the same, except for the sr no. If i have a larger > molecule without symmetric hydrogens, I imagine the program will not be > able to distinguish. How should I go about making the xml file? > This is what I have right now, > <cg_molecule> > <name>CG_WATER</name> > <ident>H2O1</ident> > <topology> > <cg_beads> > <cg_bead> > <name>b1</name> > <type>b</type> > <symmetry>1</symmetry> > <mapping>M1</mapping> > <beads> 1:H2O1:H2 1:H2O1:O1 1:H2O1:H2 > </beads> > </cg_bead> > </cg_beads> > </topology> > <maps> > <map> > <name>M1</name> > <weights> 1 16 1</weights> > </map> > </maps> > </cg_molecule> > > When I run *csg_map* --top sys.data > WARNING: The votca lammps data reader is only able to read lammps files > formatted in the following styles: > angle > atom > bond > full > molecule > > These styles use the following formats in the atom block: > atom-ID molecule-ID atom-type charge x y z > atom-ID molecule-ID atom-type charge x y z nx ny nz > atom-ID molecule-ID atom-type x y z > atom-ID molecule-ID atom-type x y z nx ny nz > atom-ID atom-type x y z > atom-ID atom-type x y z nx ny nz > > I have 2187 beads in 729 molecules > cannot find: <1:H2O1:H2> in H2O1 > an error occurred: > mapping error: molecule 1:H2O1:H2 does not exist > > Where is the error taking place here? > On Monday, February 21, 2022 at 12:44:53 PM UTC-5 Christoph Junghans wrote: > >> On Mon, Feb 21, 2022 at 9:59 AM Satyen Dhamankar <[email protected]> >> wrote: >> > >> > Hello, >> > >> > I believe this question has been asked quite a few times, but I am >> still rather in the dark regarding this. How does one go from a LAMMPS dump >> file to a coarse-grained trajectory? >> > >> > Much like the tutorials, I am running my own SPCE water simulation. >> This is the form of my LAMMPS dump file: >> > ITEM: TIMESTEP >> > 111000 >> > ITEM: NUMBER OF ATOMS >> > 2187 >> > ITEM: BOX BOUNDS pp pp pp >> > -1.3011386691164584e-01 2.8130113866912254e+01 >> > -1.3011386691164584e-01 2.8130113866912254e+01 >> > -1.3011386691164584e-01 2.8130113866912254e+01 >> > ITEM: ATOMS id type mol xu yu zu >> > 1 1 1 15.9191 21.2231 7.26312 >> > 2 2 1 15.1846 20.9848 7.89853 >> > 3 2 1 15.9358 20.5644 6.51092 >> > 4 1 2 9.47096 4.06014 23.0485 >> > 5 2 2 9.95291 3.43993 23.6674 >> > 6 2 2 9.25497 4.90974 23.5296 >> > 7 1 3 -3.19525 17.8848 16.2274 >> > 8 2 3 -3.73498 18.5917 15.7703 >> > 9 2 3 -2.992 18.1735 17.163 >> > ... >> > Now, just looking at this trajectory, my molecule of water has no name >> in particular. So, I am not sure what to put in the <ident> tag in the >> water.xml file. In the spce tutorial, the csg_map command uses topol.tpr >> for topology. But it does not seem like sys.data files which define a >> lammps topology is accepted. >> > >> > This is my sys.data file: >> > 2187 atoms >> > 2 atom types >> > 1458 bonds >> > 1 bond types >> > 729 angles >> > 1 angle types >> > 0 dihedrals >> > 0 dihedral types >> > >> > 0.0000000000000000e+00 2.8000000000000000e+01 xlo xhi >> > 0.0000000000000000e+00 2.8000000000000000e+01 ylo yhi >> > 0.0000000000000000e+00 2.8000000000000000e+01 zlo zhi >> > >> > Masses >> > >> > 1 15.99940 # OSPCe >> > 2 1.00800 # HSPCe >> > >> > Atoms >> > >> > 1 1 1 -0.82000 26.4795641655 13.9845510766 10.8342774813 0 0 0 >> > 2 1 2 0.41000 26.0120845362 13.3829183164 11.4331512727 0 0 0 >> > 3 1 2 0.41000 26.3193693668 14.8622934936 11.2114417372 0 0 0 >> > 4 2 1 -0.82000 14.0145593114 1.5446899105 26.5086662016 0 0 0 >> > 5 2 2 0.41000 14.6271886820 1.6095611553 25.7605846713 0 0 0 >> > 6 2 2 0.41000 13.1417198035 1.6740140444 26.1089494746 0 0 0 >> > 7 3 1 -0.82000 4.6668218860 23.2721041307 17.0845511689 0 0 0 >> > >> > The pdb file I use to generate the water is: >> > COMPND UNNAMED >> > AUTHOR GENERATED BY OPEN BABEL 2.3.90 >> > HETATM 1 O HOH 1 0.154 1.797 0.015 1.00 0.00 OSPCe >> > HETATM 2 H HOH 0 1.122 1.767 -0.020 1.00 0.00 HSPCe >> > HETATM 3 H HOH 0 -0.125 1.206 -0.700 1.00 0.00 HSPCe >> > CONECT 1 2 3 >> > CONECT 2 1 >> > CONECT 3 1 >> > MASTER 0 0 0 0 0 0 0 0 3 0 3 0 >> > END >> > >> > How should one proceed with LAMMPS? Is there a specific way one should >> set up topology in the event I have to run a CG simulation? >> I guess the first question is more for the lammps mailing list/ >> MatSci.org forum in the lammps section. They will know better how to >> run an SPCE simulation in LAMMPS. We provide input files for gromacs >> in the atomistic/ folder. If you are using the docker container you >> should have gromacs installed already. >> >> For the second question, to run a cg simulation you will need to >> create a cg initial condition, input settings file (settings.xml), >> target rdf and lammps script (in file) >> >> To generate the initial condition you can map an atomic file on a cg >> one using csg_map with a mapping file. (csg_map --top atomic.data --cg >> mapping.xml --trj atomic.data --out cg.dump) >> >> The mapping file is something you need to write by hand or you can use >> the stock tool (http://stock.cmm.ki.si/smt/). You can run csg_dump >> --top atomic.data to see what votca reads as molecule name and bead >> types to use in the mapping file. >> >> The target rdf you can calculate with csg_stat --top atomic.data --cg >> mapping.xml --trj atomic_traj.dump --options settings.xml >> >> The csg manual (https://www.votca.org/csg/index.html) has a section >> about input files as well. >> >> Hope that helps, >> >> Christoph >> > >> > I would appreciate any advice you have for me. >> > >> > -- >> > Join us on Slack: https://join.slack.com/t/votca/signup >> > --- >> > 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/901cde37-475f-400e-92ed-df18ed63baden%40googlegroups.com. >> >> >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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