Hello,
We are having a problem with the non-bond energy calculation in MD
simulations using Gromacs 6.4.1. Our system is a simple alumina crystal and
the non-bond interactions are defined with our own buckingham potentials.
Everything works fine when the group cutoff scheme is used. But with
similar settings in Verlet scheme, the simulation would blow up right after
step 0 showing absurdly high buckingham energy and kinetic energy.
I've tried modifying parameters related to the Verlet scheme, such as
verlet-buffer-drift, vdw-modifier and rvdw-switch, but with no luck. I also
compared the outputs from group and Verlet schemes but couldn't see
anything weird. I suspect that we made some mistakes in setting up the
topology, but couldn't figure out what might be wrong. I attached the
topology and pasted below the parameters copied from the output. I would
greatly appreciate any suggestions. Thanks in advance!
Input Parameters:
integrator = md
nsteps = 1000000
init-step = 0
cutoff-scheme = Verlet
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 500
comm-mode = Linear
nstlog = 500
nstxout = 0
nstvout = 1000
nstfout = 0
nstcalcenergy = 100
nstenergy = 500
nstxtcout = 1000
init-t = 0
delta-t = 0.0005
xtcprec = 1e+08
fourierspacing = 0.12
nkx = 32
nky = 32
nkz = 32
pme-order = 6
ewald-rtol = 1e-05
ewald-geometry = 0
epsilon-surface = 0
optimize-fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = V-rescale
bPrintNHChains = FALSE
nsttcouple = 1
epc = Berendsen
epctype = Isotropic
nstpcouple = 1
tau-p = 0.01
ref-p (3x3):
ref-p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref-p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
compress (3x3):
compress[ 0]={ 5.00000e-06, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 5.00000e-06, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 5.00000e-06}
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
verlet-buffer-drift = 0.005
rlist = 1.219
rlistlong = 1.219
nstcalclr = 1
rtpi = 0.05
coulombtype = PME
coulomb-modifier = None
rcoulomb-switch = 0
rcoulomb = 1.2
vdwtype = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 1.1
rvdw = 1.2
epsilon-r = 1
epsilon-rf = inf
tabext = 1
implicit-solvent = No
gb-algorithm = Still
gb-epsilon-solvent = 80
nstgbradii = 1
rgbradii = 1
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
DispCorr = No
bSimTemp = FALSE
free-energy = no
nwall = 0
wall-type = 9-3
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = no
rotation = FALSE
disre = No
disre-weighting = Conservative
disre-mixed = FALSE
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orires-fc = 0
orires-tau = 0
nstorireout = 100
dihre-fc = 0
em-stepsize = 0.01
em-tol = 10
niter = 20
fc-stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake-tol = 0.0001
lincs-order = 4
lincs-warnangle = 30
lincs-iter = 1
bd-fric = 0
ld-seed = 1993
cos-accel = 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}
adress = FALSE
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 10959
ref-t: 700
tau-t: 0.1
anneal: No
ann-npoints: 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm-opts:
ngQM = 0
Using 1 MPI thread
Using 1 OpenMP thread
Detecting CPU-specific acceleration.
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU E5645 @ 2.40GHz
Family: 6 Model: 44 Stepping: 2
Features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid
pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3
Acceleration most likely to fit this hardware: SSE4.1
Acceleration selected at GROMACS compile time: SSE4.1
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G.
Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.219 Coulomb: 1.2 BHAM: 1.2
Determining largest Buckingham b parameter for table
Buckingham b parameters, min: 0, max: 45.6204
System total charge: 0.000
Generated table with 4438 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4438 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4438 data points for EXPMIN.
Tabscale = 43.84 points/nm
Using SSE4.1 4x2 non-bonded kernels
Using full Lennard-Jones parameter combination matrix
Potential shift: LJ r^-12: 0.112 r^-6 0.335, Ewald 0.000e+00
Initialized non-bonded Ewald correction tables, spacing: 7.23e-04 size: 3072
Removing pbc first time
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------
There are: 3654 Atoms
Initial temperature: 699.927 K
Started mdrun on node 0 Wed Mar 13 18:32:37 2013
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Buck.ham (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
5.03375e+11 -1.27701e+07 2.74229e+03 5.03363e+11 3.10221e+15
Total Energy Temperature Pressure (bar)
3.10272e+15 6.80916e+13 8.55442e+14
--
Bu
--
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