Dear users, I've run a water membrane model through minimization, nvt, and npt with pressure coupling = surface tension with compression 4.5e-5 4 0 and with 4.5e-5 4.5e-5. I wanted to increase the box size in the z direction to created an air ( really vacuum ) interface. The membrane is in the middle of the box so there are two interfaces. After the three runs, gmx energy tells me the energy of the system is Coulomb-14 -1.15883e+06 160 495.912 318.314 (kJ/mol) Potential -1.9882e+06 7000 14892.4 -45168.4 (kJ/mol) Kinetic En. 592281 45 2027.77 305.09 (kJ/mol) Total Energy -1.39592e+06 7000 15068.9 -44863.3 (kJ/mol)
But then with or without increasing the box size and running the output of the above model with the the same npt used above or with nvt and with velocity continuation, an error is produced: Step 0: The total potential energy is 8.43672e+15, which is extremely high. The LJ and electrostatic contributions to the energy are 8.43672e+15 and -192065, respectively. A very high potential energy can be caused by overlapping interactions in bonded interactions or very large coordinate values. Usually this is caused by a badly- or non-equilibrated initial configuration, incorrect interactions or parameters in the topology. So, the npt.mdp file which works with or without z compression the first time but not the second is given below I'll try longer eq time, but why would the pot'l energy output change between runs ? Thanks Paul Buscemi BICB, UMN ============================== define = -DPOSRES ; position restrain the protein ; Run parameters integrator = sd nsteps = 500000 ; 2 * 50000 = 100 ps dt = 0.002; ; Output contro nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 5000 ; Bond parameters continuation = yes constraint_algorithm = lincs constraints = h-bonds lincs_iter = 1 lincs_order = 4 ; Neighborsearching cutoff-scheme = Verlet ns_type = grid nstlist = 20.0 rvdw = 1.0 vdw-type = cut-off verlet-buffer-tolerance = 1.4e-4 ; Electrostatics coulombtype = PME pme_order = 4 fourierspacing = 0.12 ; Temperature coupling is on tcoupl = V-rescale tc-grps = H2O MEM DrG tau_t = 0.1 0.1 .1 ref_t = 300 300 300 ; Pressure coupling is on pcoupl = Berendsen ; Parrinello-Rahman pcoupltype = surface-tension tau_p = 2.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ; or 4.5e-5 0 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; no = Velocity generation is off ******************************* gen-temp = 200 -- 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.
