[gmx-users] Help me with energy groups please.

[Dan Sponseller]

For my main MD experiment, I run just the energy group System. This is fine. Then I take one configuration and run a minimization. For the minimization, I have two energy groups: peg2000 (my polymer), and Water so that I can inspect interaction energies.

Here is the output from gmx energy:

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Morse                       13.8929         11    92.2316   -69.4839  (kJ/mol)
G96Angle                    347.715         62    127.946   -413.973  (kJ/mol)
Proper Dih.                 128.924       0.55    1.13049     -3.826  (kJ/mol)
LJ-14                       71.4762          2    4.16065   -13.8959  (kJ/mol)
Coulomb-14                  988.758       0.12   0.239868   0.836523  (kJ/mol)
LJ (SR)                      326321        2.9     5.9749   -20.3545  (kJ/mol)
Coulomb (SR)             -1.85621e+06       0.36    0.80798   -2.48026  (kJ/mol)
Coul. recip.                2094.03      0.015  0.0317153  0.0976681  (kJ/mol)
LJ recip.                  -30437.1     0.0032 0.00707587 -0.0217548  (kJ/mol)
Potential                -1.55669e+06         78    191.241   -523.261  (kJ/mol)
Pressure                 -2.80437e+34    5.7e+27 1.27529e+28 3.80388e+28  (bar)
#Surf*SurfTen            -1.35113e+33    1.8e+29 3.66158e+29 1.18298e+30  (bar nm)
Coul-SR:peg2000-peg2000  -1.85621e+06       0.36    0.80798   -2.48026  (kJ/mol)
LJ-SR:peg2000-peg2000        326321        2.9     5.9749   -20.3545  (kJ/mol)
Coul-14:peg2000-peg2000     988.758       0.12   0.239868   0.836523  (kJ/mol)
LJ-14:peg2000-peg2000       71.4762          2    4.16065   -13.8959  (kJ/mol)
Coul-SR:peg2000-Water             0          0          0          0  (kJ/mol)
LJ-SR:peg2000-Water               0          0          0          0  (kJ/mol)
Coul-14:peg2000-Water             0          0          0          0  (kJ/mol)
LJ-14:peg2000-Water               0          0          0          0  (kJ/mol)
Coul-SR:Water-Water               0          0          0          0  (kJ/mol)
LJ-SR:Water-Water                 0          0          0          0  (kJ/mol)
Coul-14:Water-Water               0          0          0          0  (kJ/mol)
LJ-14:Water-Water                 0          0          0          0  (kJ/mol)



ddd
It appears I have no interaction energy between my polymer and the water and there is no interaction energy intra-Water. This makes no sense! I am using the standard spce water witch does have partial charges and my polymer has partial charges. There should be coulomb interaction and there should always be LJ interaction.

Help me figure this out please. Attached is my mdp file.

Dan Sponseller


** Run Control **
integrator               = steep
nsteps                   = 10000
comm-mode                = Linear
nstcomm                  = 100

** Energy Minimization
emtol                    = 0.001
emstep                   = 0.01

** Output Control **
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 0
nstcalcenergy            = 10000
nstenergy                = 10000
energygrps               = peg2000 Water

** Neighbor Searching **
cutoff-scheme            = Verlet
nstlist                  = 20
ns_type                  = grid
pbc                      = xyz
periodic-molecules       = no
verlet-buffer-tolerance  = 0.001

** Electrostatics **
coulombtype              = PME
coulomb-modifier         = Potential-shift-Verlet
rcoulomb                 = 1.5

** VdW **
vdwtype                  = PME
vdw-modifier             = Potential-shift-Verlet
rvdw                     = 1.5

** Ewald **
fourierspacing           = 0.15
pme-order                = 6
ewald-rtol               = 1e-5

** Temperature Coupling **
tcoupl                   = no
;tcoupl                   = v-rescale
nsttcouple               = -1
tc-grps                  = System
tau-t                    = 1.0
ref-t                    = 300

** Pressure Coupling **
pcoupl                   = no
;pcoupl                   = Parrinello-Rahman
;pcoupl                   = Berendsen
pcoupltype               = isotropic
nstpcouple               = -1
tau-p                    = 2.0
compressibility          = 4.5e-5
ref-p                    = 1
refcoord-scaling         = all

** Velocity Generation **
gen-vel                  = no
gen-temp                 = 300
gen-seed                 = 4242

** Bonds **
constraints              = none
morse                    = yes