Hi Dan, welcome.
2014-10-20 4:37 GMT-06:00 Daniel Allen <[email protected]>: > Hi there, > > I am trying to read in a LAMMPS dump file for a simulation of liquid butane > into csg_stat as a simple example of how to map and process LAMMPS > trajectories, before moving onto my more complex system of long chain > polymers. > > I know that there are a couple of previous questions regarding LAMMPS > topologies but I cannot quite get it working. > > First I tried using a .pdb file specified in my topol.xml file but this gave > an error: > > "an error occurred: > P-P.pdb: unknown topology format" which I find strange because in the manual > it gives an example of using a pdb file for topology, any ideas why this > error would occur? Which version of VOTCA is that? In 1.2 the pdb is based on the gromacs reader, which means without Gromacs you won't be able to use pdb files. However in 1.3 the pdb reader is independent from the Gromacs library, so make sure you have the 1.3-dev version installed before going on: <https://code.google.com/p/votca/wiki/Installing#Development_Version> Also the lammps dump reader in 1.3 is a bit more versatile. > > Anyway, I then decided to try and use the lammps .dump file as the topology > so topol.xml now looks like this: > > <topology base="atoms_nvt_prod.dump">/ITEM > <molecules> > <clear/> > <define name="B" first="1" nbeads="14" nmols="100"/> > </molecules> > </topology> > > So I have defined one molecule type which consists of 14 atoms and there are > 100 molecules in the system beginning at atom 1. > > I think the problem lies in the coarse-grained mapping file. When listing > atoms which belong to a particular bead, if the syntax is > RESID:RESNAME:ATOMNAME then I'm struggling to work out what they should be > for my system. > > Here is the top of my dump file: > > ITEM: TIMESTEP > 0 > ITEM: NUMBER OF ATOMS > 13916 > ITEM: BOX BOUNDS pp pp pp > -27.8209 27.7639 > -27.7926 27.8726 > -27.6615 27.7715 > ITEM: ATOMS id type x y z > 12765 2 -21.1019 -18.5716 -26.1089 > 12766 1 -21.1227 -18.563 -24.9982 > 12768 1 -20.1424 -19.0188 -26.4462 > 9768 1 -25.3608 -20.7513 -21.6347 > 9766 2 -25.8077 -20.8022 -20.6188 > 9762 1 -23.0727 -20.4904 -19.9854 > 9764 1 -25.494 -18.664 -19.9916 > 9763 2 -25.1286 -19.6941 -19.7923 > 9767 1 -26.8648 -20.4951 -20.7686 > 9769 2 -25.9722 -22.1004 -19.9808 > 9760 1 -23.565 -19.281 -21.2077 > 9759 2 -23.6425 -19.548 -20.132 > 13105 2 -25.5908 -19.0274 -24.4098 > 638 2 -22.4319 -26.8526 -26.9045 > 9772 1 -26.1693 -22.9545 -20.6634 > 13106 1 -25.5393 -19.9713 -24.9935 > 11466 1 -22.2057 -26.6297 -23.7546 > 11454 1 -26.0494 -24.6427 -23.5225 > 11458 1 -24.8424 -26.6034 -24.4689 > 3362 1 -20.4076 -20.3751 -20.0356 > 639 1 -22.2076 -27.6125 -26.1257 > > etc ... > > Would RESID just be 1? There is no information about residues in the dump > file, does there need to be? It is possible to printout the molecule number > in the dump file. > > For RESNAME, I wouldn't know what to use either. > > For ATOMNAME I could use the atom type, so atom name would be "2" for C and > "1" for H? > > The choice for these labels would be more obvious from my .pdb file: > > > HETATM 1 C7 B A 1 -5.985 7.723 -2.9591.00 0.00 > C > HETATM 2 H71 B A 1 -5.479 7.242 -2.1481.00 0.00 > H > HETATM 3 H72 B A 1 -5.406 7.617 -3.8531.00 0.00 > H > HETATM 4 C8 B A 1 -6.944 7.270 -3.1001.00 0.00 > C > HETATM 5 C9 B A 1 -7.523 7.376 -2.2061.00 0.00 > C > HETATM 6 H81 B A 1 -6.818 6.231 -3.3221.00 0.00 > H > HETATM 7 H82 B A 1 -7.450 7.750 -3.9111.00 0.00 > H > HETATM 8 H91 B A 1 -7.017 6.896 -1.3951.00 0.00 > H > HETATM 9 C10 B A 1 -8.482 6.923 -2.3471.00 0.00 > C > HETATM 10 H92 B A 1 -7.648 8.415 -1.9831.00 0.00 > H > HETATM 11 H101 B A 1 -8.357 5.884 -2.5691.00 0.00 > H > HETATM 12 H102 B A 1 -8.988 7.404 -3.1581.00 0.00 > H > HETATM 13 H73 B A 1 -6.112 8.781 -2.7321.00 0.00 > H > HETATM 14 H103 B A 1 -9.071 7.031 -1.4361.00 0.00 > H > > So for the first atom it would be 1:B:C7 for example? You can simply run $ csg_dump --top topol.xml to see how VOTCA see and how it names the beads. The residue name/number doesn't really matter as long as the triple "RESID:RESNAME:ATOMNAME" is unique for every bead. Cheers, Christoph > > > Any help would be greatly appreciated, > > Thanks, Dan. > > > > > > -- > 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 http://groups.google.com/group/votca. > 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
