[gmx-users] LJ-14 energy

Ming Tang m21.tang at qut.edu.au
Wed Jul 15 11:43:21 CEST 2015

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?

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?

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.


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