Hi all,
I am simulating a system with two slabs and water molecules in between. The slabs were frozen during simulations and I've exclude the interactions between slab atoms. After energy minimization, I run nvt at 300 K for 10 ns, followed by annealing the system to 250 K in 1 ns. Then another nvt was run at 250 K for 6 ns. So far, everything was normal. Then I switched to nve simulation by turning off the thermostat. However, the energy of the system kept decreasing (temperature was reaching 0 K). I was using Group cut-off for all the simulations. I've checked the energy between different groups. The energies between slab and slab, both coulombic and LJ are 0, which make sense because I've exclude the interactions. The energies between water and water, on the other hand, decreased to a huge extend. I am not sure why this happened. If I remove the slabs, only simulate water molecules, then it works just fine. Please let me know if you have ever encountered such problem. Any suggestions would be greatly appreciated. I am using Gromacs/5.1.4 and the parameters in .mdp file are listed as follows: Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 25000000 init-step = 0 simulation-part = 1 comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 603782470 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 250000 nstvout = 250000 nstfout = 0 nstlog = 250000 nstcalcenergy = 100 nstenergy = 250000 nstxout-compressed = 0 compressed-x-precision = 1000 cutoff-scheme = Group nstlist = 10 ns-type = Grid pbc = xyz periodic-molecules = FALSE verlet-buffer-tolerance = 0.005 rlist = 1 rlistlong = 1 nstcalclr = 0 coulombtype = PME coulomb-modifier = None rcoulomb-switch = 0 rcoulomb = 1 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = None rvdw-switch = 0 rvdw = 1 DispCorr = EnerPres table-extension = 1 fourierspacing = 0.16 fourier-nx = 36 fourier-ny = 36 fourier-nz = 48 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 0 epsilon-surface = 0 implicit-solvent = No gb-algorithm = Still nstgbradii = 1 rgbradii = 1 gb-epsilon-solvent = 80 gb-saltconc = 0 gb-obc-alpha = 1 gb-obc-beta = 0.8 gb-obc-gamma = 4.85 gb-dielectric-offset = 0.009 sa-algorithm = Ace-approximation sa-surface-tension = 2.05016 tcoupl = No nsttcouple = -1 nh-chain-length = 0 print-nose-hoover-chain-variables = FALSE pcoupl = No pcoupltype = Isotropic nstpcouple = -1 tau-p = 1 compressibility (3x3): compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p (3x3): ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} refcoord-scaling = No posres-com (3): posres-com[0]= 0.00000e+00 posres-com[1]= 0.00000e+00 posres-com[2]= 0.00000e+00 posres-comB (3): posres-comB[0]= 0.00000e+00 posres-comB[1]= 0.00000e+00 posres-comB[2]= 0.00000e+00 QMMM = FALSE QMconstraints = 0 QMMMscheme = 0 MMChargeScaleFactor = 1 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = TRUE Shake-SOR = FALSE shake-tol = 0.0001 lincs-order = 6 lincs-iter = 1 lincs-warnangle = 30 nwall = 0 wall-type = 9-3 wall-r-linpot = -1 wall-atomtype[0] = -1 wall-atomtype[1] = -1 wall-density[0] = 0 wall-density[1] = 0 wall-ewald-zfac = 3 pull = FALSE rotation = FALSE interactiveMD = FALSE disre = No disre-weighting = Conservative disre-mixed = FALSE dr-fc = 1000 dr-tau = 0 nstdisreout = 100 orire-fc = 0 orire-tau = 0 nstorireout = 100 free-energy = no cos-acceleration = 0 deform (3x3): deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00} simulated-tempering = FALSE E-x: n = 0 E-xt: n = 0 E-y: n = 0 E-yt: n = 0 E-z: n = 0 E-zt: n = 0 swapcoords = no adress = FALSE userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 24285 ref-t: 0 tau-t: 0 annealing: No annealing-npoints: 0 acc: 0 0 0 nfreeze: Y Y Y N N N energygrp-flags[ 0]: 1 0 energygrp-flags[ 1]: 0 0 Thanks again and best regards, Yi -- 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.