Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule "AcO" starting from a structure in which they are non-covalently interacting. I'm using the AMBER99 forcefield with GAFF. I've confirmed by visual inspection that the molecules are interacting with each other, i.e. they didn't separate during the simulation. Additionally, I've specified the energy groups "aco_1", "aco_2", "SOL", "Ion" in the original MD tpr. The problem is that g_energy reports all "aco_1-aco_2" energy terms as exactly 0.000000. The energy terms are OK.
This was only an example. I actually simulated 2, 3 and 4 copies of interacting molecules in different ways and this happens in all cases. These results were obtained using GPUs. I used the same .tpr to rerun the .xtc on CPUs only and now the "aco_1-aco_2" energy terms are OK. In both cases I used GROMACS 4.6.6. I've searched the list but found nothing. Is this a problem/bug? Am I doing something wrong with the GPUs? Thank you in advance, Leandro -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.