Dear all, I have run a CG-MD simulation and output energies of different energy groups. When I run g_energy to get some of the energy terms out I input the number of molecules in my system -nmol "X" (X = Y number of water molecules (beads) + Z number of proteins + W number of lipids), to make sure that I get the correct value of kJ/mol.
Firstly, I am wondering if the number of water molecules (Y) should be the number of beads, or the number of real water molecules it corresponds to, that is multiplied by 4? If I use the number of beads, then the number of molecules gets skewed because the number of molecules for lipids (W) and protein (Z) even after coarse-graining is still the same... Secondly, the results puzzle me a bit. Changing the -nmol number results in only the bonded energy changing. Is this correct? The remaining terms (LJ, Coul) stay the same... I am running gromacs 4.0.7 Kind regards, Jesper Soerensen -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
