On Wed, Jul 15, 2015 at 6:27 AM, Ming Tang <[email protected]> wrote: > Dear Gromacs experts, > > I am confused about the meaning of LJ-14 option in g_energy. I checked the > achieve, and found that Justin said it stands for intramolecular interactions > between atoms separated by 3 bonds. My simulation is protein solvated in > water. How can I calculate the Lennard-Jones potential energy of the whole > system? > I found that if I set 2 energy groups and rerun, there will be options like > LJ-14: protein-ions. So, how does Gromacs calculate those energy?
Yes, LJ-14 is an intramolecular term. It may be simpler to exclude this term from summation when calculation total energy. If you exclude it for one system, then obviously exclude for all other systems you compare to. > Another problem I came across is the LJ-14 I got is weird. The Coulomb-14 > energy decrease from 5e4 to 3.8e4, but LJ-14 energy decrease from -400 to > -700 and then increase to- 400, followed by a linear decline to -1700. The > LJ-14 should increase, am I right? This fully depends on which objects you have in your system. Upon which action do these terms increase? > Here is part of my .mdp > > cutoff-scheme = verlet > ns_type = grid > coulombtype = reaction-field > coulomb-modifier = potential-shift > rcoulomb-switch = 0.8 > rcoulomb = 1.4 > epsilon_rf = 61 > vdwtype = cut-off > vdw-modifier = force-switch > rvdw-switch = 0.8 > rvdw = 1.4 > > To find out the reason, I checked the manual. It says for vdwtype = switch or > vdw-modifier = Potential - switch, rlist should be 0.1 - 0.3 larger than > rvdw. As I did not set verlet-buffer-tolerance = -1, gromcas set rlist =1 for > the simulation automatically, which is not 0.1 - 0.3 larger than rvdw. Is > this the reason of the weird LJ-14? > Another question is, is vdw-modifier = force switch more accurate than > vdw-modifier = potential - shift? > > Any help will be appreciated. > > Regards > -- > 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 [email protected]. -- 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 [email protected].
