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. -- 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.
