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

[Justin Lemkul]

On 6/20/15 4:48 PM, Dan Sponseller wrote:
> 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.
>

It's probably because you're doing EM and not dynamics.  Not all dynamics 
features are enabled in EM.  That would be my first guess.  Try running a quick 
MD with the same energygrps.  If those show up correctly, you have your answer.

-Justin

> 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
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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