[gmx-users] Dynamic updating of nstlist in gromacs 5 screws up simulation results
Szilárd Páll
pall.szilard at gmail.com
Wed Jun 24 22:42:32 CEST 2015
Hi,
I think it is not very likely that the nstlist tuning would cause very
different results - especially not as a direct effect of the less
frequent pair search. With nstlist updated rlist also gets
recalculated; I've just checked and the estimates between 4.6 and 5.0
have not changed.
You can set nstlist on the command line (starting with v5.0) using the
"-nstlist" option, in v4.6 this is not exposed on the mdrun command
line interface, but it is supported through the GMX_NSTLIST
environment variable.
I suggest to try running v5.0 with -nstlist 10 and possibly also v4.6
with the increased nstlist=20.
Cheer,s
--
Szilárd
On Wed, Jun 24, 2015 at 7:53 PM, Michael Daily <mdaily.work at gmail.com> wrote:
> 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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