Hi, and welcome.
2014-09-18 19:02 GMT-06:00 Francesca Stanzione <[email protected]>: > Hi everyone, > I want to run an Adaptive resolution simulation with GROMACS. Prtaically I > want to consider the water molecules in both atomistic and coarse grained > representations. I created thje hybrid_spc.itp adding the coarse-grained > virtual site, now I want to add the virtual site coordinate ti the > coordinate file. Gromacs suggests to do taht with --hybrid option of the > csg_map. The problem is that I don't have the --hybrid option..this is what > I have: > ================================================== > ======== VOTCA (http://www.votca.org) ======== > ================================================== > > please submit bugs to [email protected] > > csg_map, version 1.2.4 hgid: 831be077efa9 (compiled Sep 18 2014, 20:26:31) > votca_tools, version 1.2.4 hgid: 9454b72de1ef (compiled Sep 18 2014, > 20:25:47) > gromacs, VERSION 4.6.5 (double precision) > > Map a reference trajectory to a coarse-grained trajectory. > This program can be used to map a whole trajectory or to > create an initial configuration for a coarse-grained run only. > > Allowed options: > -h [ --help ] produce this help message > --top arg atomistic topology file > --out arg output file for coarse-grained trajectory > > Mapping options: > --cg arg coarse graining mapping definitions (xml-file) > --map-ignore arg list of molecules to ignore separated by ; > --no-map disable mapping and act on original trajectory > > Trajectory options: > --trj arg atomistic trajectory file > --begin arg (=0) skip frames before this time > --first-frame arg (=0) start with this frame > --nframes arg process the given number of frames > > > > Is it possible that I miss something when I installed VOTCA? This is my sh The --hybrid option is currently only available in the development version (1.3-dev)! > file: > prefix=$SW/votca > mkdir -p ${prefix}/src > cd ${prefix}/src > wget http://votca.googlecode.com/hg/build.sh > chmod +x build.sh > ./build.sh --prefix ${prefix} tools csg -DWITH_GSL=OFF -DWITH_SQLITE3=OFF > -DGMX_DOUBLE=ON -DFFTW3_INCLUDE_DIR=$SW/include > -DFFTW3_LIBRARY=$SW/lib/libfftw3.so > -DGROMACS_INCLUDE_DIR=$SW/include/gromacs > -DGROMACS_LIBRARY=$SW/lib/libgmx_d.so You did all right, just a "--dev" option to your build command line. Also see: <https://code.google.com/p/votca/wiki/Installing#Development_Version> Cheers, Christoph > > > Any suggestions?? > Thank you, > Francesca > > -- > 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.
