On Sat, Jun 23, 2018 at 4:40 PM, Eduardo A <[email protected]> wrote: > Hi, thank you for your reply > > I have another question about how to include the coarse grained particles in > the coordinate file for gromacs (.gro) for an adaptive resolution > simulation. I've read in the gromacs manual (version 5.1.5) that this > coordinate file containing the coarse-grained sites for every molecule > (water, in my case) can be created with the csg_map function of VOTCA with > the --hybrid option enabled. The output would be something like: > > adaptive water coordinates > > 34028 > > 1SOL OW 1 0.283 0.886 0.647 > 1SOL HW1 2 0.359 0.884 0.711 > 1SOL HW2 3 0.308 0.938 0.566 > 1SOL CG 4 0.289 0.889 0.646 > 1SOL OW 5 1.848 0.918 0.082 > 1SOL HW1 6 1.760 0.930 0.129 > 1SOL HW2 7 1.921 0.912 0.150 > 1SOL CG 8 1.847 0.918 0.088 > (...) > > where each coarse-grained site is located in the center of mass of the > water molecule. My problem is that I'm not being able to generate this file. > csg_map requires a topology file in .tpr format and when I try to create it > with grompp it gives me an error that the CG particles indicated in the .top > file cannot be found. So, I'm confused. I would appreciate if you could help > me showing how could I make this hybrid coordinate file. Just the files from the spce/atomistic folder in csg-tutorials: $ cd csg-tutorials/spce/atomistic $ gmx grompp $ csg_map --top topol.tpr --cg water.xml --trj conf.gro --out conf_hy.gro --hybrid
Christoph > > -- > 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 https://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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
