Re: [gmx-users] angular COM removal

Hallo Maybe try comm-grps = protein all-but-protein (all-but-protein being all atoms except those contained in protein) I guess this problem is brought about by the way VCM groups are constructed: src/kernel/readir.c, do_numbering(), line 1081 in 4.0.3 if (grps->nr == 1) { groups->ngrpnr[gt

Re: [gmx-users] problem with ffamber94bon.itp

hi the file ffamber94bon.itp defines the parameters as macros. some of the macro names contain an asterisk character (*), e.g. #define proper_X_CT_N*_X 0.0 0.0 0.0 0.0 0.0 0.0 this makes the preprocessor issue a warning (no whitespace after macro na

Re: [gmx-users] Hessian instability

Ignacio Rodriguez Fernandez wrote: Hello, I´m trying perform a normal mode analysis of a large molecule. My problem is that I always get negative eigenvalues, which shouldn´t happen in theory. The problem seems to be the instability of the Hessian matrix, due to an unproper minimization of the