[gmx-users] Topology for covalent bonds across periodic boundaries

For example, the following dihedral did not return an error: (179THR N 2649 )-(179THR CA 2651 )-(179THR C 2661 )-(0ALA N1 ) However, this dihedral did: (179THR CA 2651 )-(179THR C 2661 )-(0ALA N1 )-(0ALA HN2 ) Any help in debugging this w

[gmx-users] Topology errors: covalent bonds across periodic boundaries

For example, the following dihedral did not return an error: (179THR N 2649 )-(179THR CA 2651 )-(179THR C 2661 )-(0ALA N1 ) However, this dihedral did: (179THR CA 2651 )-(179THR C 2661 )-(0ALA N1 )-(0ALA HN2 ) Any help in debugging this w

[gmx-users] Parallelization in large system

atoms), which ran without incident on a 1D domain decomposition grid 8 x 1 x 1. What parameters do you recommend I change to allow for multithreading? Thank you in advance, Rachel Baarda -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX