[gmx-users] Energy conservation problem in NVE simulation for a system with frozen atoms
Yi Ren
yiren at chem.ubc.ca
Thu May 9 01:45:09 CEST 2019
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
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