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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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 gmx-users-requ...@gromacs.org.
