2013/9/10 Scott Sides <[email protected]>: > Christoph, > > Thanks for all your help. I've got the ibi_lammps example running for > spce water. > I can see the g(r) calculated converge on the target g(r) as the U(r) for > the water is > changed. Currently, the lammps example still needs the spce.gro file (its > listed in the > topology file) Why is this? Is there a way of re-writing the topol.xml file > so only LAMMPS > files are used? The lammps interface is pretty new and hence not all things are as smooth as in the case of gromacs, which VOTCA was build around. VOTCA supports several topology formats like xyz, lammps dumps and xml files. However, not all of them have molecules or even atom names specified, which makes some things hard when it comes to mappings (csg_map or csg_inverse with bonded interactions).
It is relatively easy write a new topology reader, existing ones can be found here: <https://code.google.com/p/votca/source/browse/src/libcsg/modules/io/lammpsreader.cc?repo=csg> Testing a topology file can be done with $ csg_dump --top FILE.EXT Depending on what you need the lammps topology could be improved: <https://code.google.com/p/votca/source/browse/src/libcsg/modules/io/lammpsreader.cc?repo=csg> Another option would be to make the pdb reader independent of libgmx, because a pdb has at least atom names, which then can be made into types using it as a base of an xml topology. Christoph > > Thanks, > Scott > > On Monday, September 9, 2013 10:34:44 AM UTC-6, Christoph Junghans wrote: >> >> 2013/9/9 Scott Sides <[email protected]>: >> > Christoph, >> > >> > I should say that I'm using my own build system that is used to manage >> > large build chains (I'm using this for LAMMPS, PolySwift++ and other >> > codes) >> > so I wont be using the votca build scripts. >> I see. >> > >> > Did your update include changes that are not included completely in >> > the >> > r2135 >> > version? Is there a patch file of some sort I need to pull as well? >> csg-tutotorials is a different repository like VOTCA tools. >> >> As there is nothing to build in csg-tutorials, you can just do: >> hg clone https://code.google.com/p/votca.csg-tutorials >> >> >> > >> > Scott >> > >> > On Friday, September 6, 2013 12:10:00 PM UTC-6, Scott Sides wrote: >> >> >> >> I'm running the tutorial for inverse boltzmann on spce water for >> >> lammps. >> >> I've got >> >> a lammps build that I know is running. >> >> >> >> The files are in 'csg-tutorials.votca-8d845530808b/spce/ibi_lammps' >> >> >> >> When I run csg_inverse --options settings.xml I get >> >> >> >> >> >> >> >> ########################################################################################################## >> >> # >> >> # >> >> # ERROR: >> >> # >> >> # critical: 'lmp -in spce.in' failed >> >> # >> >> # For details see the logfile >> >> >> >> /Users/ssides/csg-tutorials.votca-8d845530808b/spce/ibi_lammps/inverse.log >> >> # >> >> # >> >> # >> >> >> >> >> >> ########################################################################################################## >> >> >> >> When I simply try 'lmp -in spce.in' I get >> >> >> >> LAMMPS (14 Aug 2013) >> >> Reading data file ... >> >> orthogonal box = (0 0 0) to (4.031 4.031 4.031) >> >> 1 by 1 by 1 MPI processor grid >> >> 2180 atoms >> >> ERROR on proc 0: Cannot open file CG_CG.pot (../pair_table.cpp:350) >> >> >> >> Clearly from the spce.in file >> >> >> >> # coarse-grained spce water >> >> >> >> units lj >> >> atom_style atomic >> >> >> >> read_data spce.data >> >> >> >> velocity all create 2.49 87287 >> >> >> >> pair_style table linear 1000 >> >> pair_coeff 1 1 CG_CG.pot VOTCA 0.9 >> >> >> >> timestep 0.001 >> >> fix 1 all nve >> >> fix 2 all langevin 2.49 2.49 0.2 545454 >> >> >> >> dump 1 all xyz 50 traj.xyz >> >> >> >> thermo 50 >> >> run 2500 >> >> ########################################################### >> >> >> >> It needs a CG_CG.pot file. However, I dont know where this file is. Do >> >> I >> >> need to copy from somewhere? >> >> >> >> Scott Sides >> >> NREL >> > >> > -- >> > 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/groups/opt_out. >> >> >> >> -- >> 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/groups/opt_out. -- 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/groups/opt_out.
