On Mon, Feb 21, 2022 at 3:08 PM Satyen Dhamankar <[email protected]> wrote: > > Furthermore, where is the resname DUM coming from? It is the residue name and as data file have no residue name, VOTCA sets it to DUM for dummy.
> > 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? I think for more complicated molecule, you will need to create xml topology file. See towards the end of https://www.votca.org/csg/input_files.html#advanced-topology-handling. You can basically do something like: $ cat topol.xml <topology> <molecules> <box xx="2.8" yy="2.8" zz="2.8" /> <molecule name="H20" nmols="729" nbeads="3"> <!-- composition of molecule, bead definition --> <bead name="O1" type="O" mass="15.9994" q="-0.82" /> <bead name="H1" type="H" mass="1.008" q="0.41" /> <bead name="H2" type="H" mass="1.008" q="0.41" /> </molecule> </topology> then you can use H20:O1 etc in the mapping file. (Check with csg_dump --top topol.xml first.) inferring all topology information from all different MD inputs is sometimes incomplete, hence we have the xml topology format. Patches for the lammps data reader are always welcome. >> 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? Can you try "0:H2O1:H2" instead? >> 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. > 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/34d4cee2-9505-46ea-9ea1-5c07f16c1cffn%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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