[gmx-users] Dynamic updating of nstlist in gromacs 5 screws up simulation results
Michael Daily
mdaily.work at gmail.com
Wed Jun 24 19:53:28 CEST 2015
Hi,
A colleague of mine and I have recently discovered that gromacs 4.6.4 and
5.0.4 give very different results in the simulation of a biomimetic polymer
using an AMBER-based force field. She found that gromacs 5 mdrun is
dynamically changing nstlist from 10 to 20 or 40 depending on the
simulation, as documented below. Is it possible that this is causing the
favored conformation of the polymer to change? Is there a way in GMX 5 to
prevent this dynamic updating from happening?
### log file ###
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------
NOTE: Error occurred during GPU detection:
CUDA driver version is insufficient for CUDA runtime version
Can not use GPU acceleration, will fall back to CPU kernels.
Changing nstlist from 10 to 20, rlist from 1 to 1.029
Input Parameters:
integrator = md
tinit = 0
dt = 0.002
nsteps = 100000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 2891701100
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 5000
nstvout = 5000
nstfout = 5000
nstlog = 5000
nstcalcenergy = 100
nstenergy = 5000
nstxout-compressed = 5000
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
ns-type = Grid
pbc = xyz
periodic-molecules = FALSE
verlet-buffer-tolerance = 0.005
rlist = 1.029
rlistlong = 1.029
nstcalclr = 10
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1
DispCorr = No
table-extension = 1
fourierspacing = 0.12
fourier-nx = 52
fourier-ny = 52
fourier-nz = 52
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 = Nose-Hoover
nsttcouple = 5
nh-chain-length = 1
print-nose-hoover-chain-variables = FALSE
pcoupl = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 10
tau-p = 1
compressibility (3x3):
compressibility[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compressibility[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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}
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 = FALSE
Shake-SOR = FALSE
shake-tol = 0.0001
lincs-order = 4
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 = no
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: 291.972 31383 29.9972 29.9972
ref-t: 300 300 300 300
tau-t: 0.2 0.2 0.2 0.2
annealing: No No No No
annealing-npoints: 0 0 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0
Initializing Domain Decomposition on 24 ranks
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.425 nm, LJ-14, atoms 11 17
multi-body bonded interactions: 0.425 nm, Proper Dih., atoms 11 17
Minimum cell size due to bonded interactions: 0.467 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.772 nm
Estimated maximum distance required for P-LINCS: 0.772 nm
This distance will limit the DD cell size, you can override this with -rcon
Guess for relative PME load: 0.20
Will use 18 particle-particle and 6 PME only ranks
This is a guess, check the performance at the end of the log file
Using 6 separate PME ranks, as guessed by mdrun
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 18 cells with a minimum initial size of 0.965 nm
The maximum allowed number of cells is: X 5 Y 5 Z 4
Domain decomposition grid 3 x 2 x 3, separate PME ranks 6
PME domain decomposition: 3 x 2 x 1
Interleaving PP and PME ranks
This rank does only particle-particle work.
Domain decomposition rank 0, coordinates 0 0 0
Using 24 MPI threads
Using 1 OpenMP thread per tMPI thread
Detecting CPU SIMD instructions.
Present hardware specification:
Vendor: GenuineIntel
Brand: Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
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
SIMD instructions most likely to fit this hardware: SSE4.1
SIMD instructions selected at GROMACS compile time: SSE4.1
No GPUs detected
Will do PME sum in reciprocal space for electrostatic interactions.
++++ 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 0.320163 nm for Ewald
Cut-off's: NS: 1.029 Coulomb: 1 LJ: 1
System total charge: 0.000
Generated table with 1014 data points for Ewald.
Tabscale = 500 points/nm
Generated table with 1014 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 1014 data points for LJ12.
Tabscale = 500 points/nm
Generated table with 1014 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1014 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1014 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Using SSE4.1 4x4 non-bonded kernels
Using Lorentz-Berthelot Lennard-Jones combination rule
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald correction tables, spacing: 9.33e-04 size: 2176
Removing pbc first time
Pinning threads with an auto-selected logical core stride of 1
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------
The number of constraints is 152
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Linking all bonded interactions to atoms
There are 16397 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1 Y 1 Z 1
The initial domain decomposition cell size is: X 1.66 nm Y 2.49 nm Z 1.44 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.029 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.029 nm
multi-body bonded interactions (-rdd) 1.029 nm
atoms separated by up to 5 constraints (-rcon) 1.437 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1 Z 1
The minimum size for domain decomposition cells is 1.029 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.62 Y 0.41 Z 0.72
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.029 nm
two-body bonded interactions (-rdd) 1.029 nm
multi-body bonded interactions (-rdd) 1.029 nm
atoms separated by up to 5 constraints (-rcon) 1.029 nm
Making 3D domain decomposition grid 3 x 2 x 3, home cell index 0 0 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 15861 Atoms
Charge group distribution at step 0: 853 904 881 863 893 859 857 913 880
866 892 881 893 888 889 884 888 877
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 299.753 K
Started mdrun on rank 0 Wed Mar 4 19:25:32 2015
Step Time Lambda
0 0.00000 0.00000
--
====================================
Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
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