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 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.
