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/CAHG27e5jT783KH8jyCci8CAY9AbyVrQiqDFEFBXDCrfZNvTbow%40mail.gmail.com.
