[gmx-developers] Drift in Conserved-Energy with Nose-Hoover thermostat

Bernhard Reuter b.reuter at uni-kassel.de
Sun Jul 19 22:14:55 CEST 2015


Dear David,

I am using a time step of 1fs.

Best,
Bernhard

-- 
Dipl.-Phys. Bernhard Reuter
Institute of Physics
Theoretical Physics - University of Kassel
Heinrich-Plett-Str. 40
34132 Kassel  -  Germany
Tel.: +49-561-804-4482
Email: b.reuter at uni-kassel.de

Am 7/19/15, 9:11 PM, schrieb Bernhard Reuter:
>
>
>
> -------- Weitergeleitete Nachricht --------
> Betreff: 	Re: [gmx-developers] Drift in Conserved-Energy with 
> Nose-Hoover thermostat
> Datum: 	Thu, 16 Jul 2015 00:12:33 +0200
> Von: 	David van der Spoel <spoel at xray.bmc.uu.se>
> Antwort an: 	gmx-developers at gromacs.org
> An: 	gromacs.org_gmx-developers at maillist.sys.kth.se
>
>
>
> On 15/07/15 19:01, Mark Abraham wrote:
> > Hi,
> >
> > Yes, that's a problem long fixed, and several orders of magnitude larger.
> >
> We noted the same problem a while back and in that case it was getting
> deteriorated by too short time steps, since the update of the position
> introduces loss of precision in single precision. What time step are you
> using?
>
> > Mark
> >
> > On Wed, Jul 15, 2015 at 6:16 PM Bernhard<b.reuter at uni-kassel.de
> >  <mailto:b.reuter at uni-kassel.de>> wrote:
> >
> >     I remember some research articlehttp://dx.doi.org/10.1063/1.2431176  (or
> >https://www.deshawresearch.com/publications/A%20common,%20avoidable%20source%20of%20error%20in%20molecular%20dynamics%20integrators.pdf)
> >     from 2006 which showed a comparable linear energy drift for single
> >     precision GROMACS 3.3.1 due to not optimal calculation of the velocity
> >     of constrained particels.
> >     But this issue should be solved in version 4.6.7?
> >
> >     Best,
> >     Bernhard
> >
> >     Am 15/07/15 um 18:04 schrieb Bernhard:
> >      > Indeed seems so... unfortunately I have no clue about the cause.
> >      > Maybe the head of the .log file is of some use?
> >      >
> >      > Log file opened on Wed Jul  1 17:33:48 2015
> >      > Host: theo2-pc20  pid: 15411  nodeid: 0  nnodes:  1
> >      > Gromacs version:    VERSION 4.6.7
> >      > Precision:          single
> >      > Memory model:       64 bit
> >      > MPI library:        thread_mpi
> >      > OpenMP support:     enabled
> >      > GPU support:        disabled
> >      > invsqrt routine:    gmx_software_invsqrt(x)
> >      > CPU acceleration:   AVX_256
> >      > FFT library:        fftw-3.3.2-sse2
> >      > Large file support: enabled
> >      > RDTSCP usage:       enabled
> >      > Built on:           Di 16. Jun 15:38:40 CEST 2015
> >      > Built by:           berni at theo2-pc20 [CMAKE]
> >      > Build OS/arch:      Linux 3.13.0-43-generic x86_64
> >      > Build CPU vendor:   GenuineIntel
> >      > Build CPU brand:    Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
> >      > Build CPU family:   6   Model: 62   Stepping: 4
> >      > Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> >      > mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd
> >     rdtscp
> >      > sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >      > C compiler:         /usr/bin/cc GNU cc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
> >      > C compiler flags:   -mavx    -Wextra -Wno-missing-field-initializers
> >      > -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> >      > -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized
> >      > -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops
> >      > -fexcess-precision=fast -O3 -DNDEBUG
> >      >
> >      >
> >      >                          :-)  G  R  O  M  A  C  S  (-:
> >      >
> >      >                       GROwing Monsters And Cloning Shrimps
> >      >
> >      >                             :-)  VERSION 4.6.7  (-:
> >      >
> >      >         Contributions from Mark Abraham, Emile Apol, Rossen
> >     Apostolov,
> >      >            Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
> >      >      Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
> >      > Junghans,
> >      >         Peter Kasson, Carsten Kutzner, Per Larsson, Pieter
> >     Meulenhoff,
> >      >            Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> >      >                 Michael Shirts, Alfons Sijbers, Peter Tieleman,
> >      >
> >      >                Berk Hess, David van der Spoel, and Erik Lindahl.
> >      >
> >      >        Copyright (c) 1991-2000, University of Groningen, The
> >     Netherlands.
> >      >          Copyright (c) 2001-2012,2013, The GROMACS development
> >     team at
> >      >         Uppsala University & The Royal Institute of Technology,
> >     Sweden.
> >      >             check outhttp://www.gromacs.org  for more information.
> >      >
> >      >          This program is free software; you can redistribute it
> >     and/or
> >      >        modify it under the terms of the GNU Lesser General Public
> >     License
> >      >         as published by the Free Software Foundation; either
> >     version 2.1
> >      >              of the License, or (at your option) any later version.
> >      >
> >      >                                 :-)  mdrun  (-:
> >      >
> >      >
> >      > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> >      > B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> >      > GROMACS 4: Algorithms for highly efficient, load-balanced, and
> >     scalable
> >      > molecular simulation
> >      > J. Chem. Theory Comput. 4 (2008) pp. 435-447
> >      > -------- -------- --- Thank You --- -------- --------
> >      >
> >      >
> >      > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> >      > D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark andH.
> >      > J. C.
> >      > Berendsen
> >      > GROMACS: Fast, Flexible and Free
> >      > J. Comp. Chem. 26 (2005) pp. 1701-1719
> >      > -------- -------- --- Thank You --- -------- --------
> >      >
> >      >
> >      > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> >      > E. Lindahl and B. Hess and D. van der Spoel
> >      > GROMACS 3.0: A package for molecular simulation and trajectory
> >     analysis
> >      > J. Mol. Mod. 7 (2001) pp. 306-317
> >      > -------- -------- --- Thank You --- -------- --------
> >      >
> >      >
> >      > ++++ 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 --- -------- --------
> >      >
> >      > Input Parameters:
> >      >    integrator           = md
> >      >    nsteps               = 10000000
> >      >    init-step            = 0
> >      >    cutoff-scheme        = Verlet
> >      >    ns_type              = Grid
> >      >    nstlist              = 10
> >      >    ndelta               = 2
> >      >    nstcomm              = 100
> >      >    comm-mode            = Linear
> >      >    nstlog               = 5000
> >      >    nstxout              = 5000
> >      >    nstvout              = 5000
> >      >    nstfout              = 0
> >      >    nstcalcenergy        = 100
> >      >    nstenergy            = 1000
> >      >    nstxtcout            = 1000
> >      >    init-t               = 0
> >      >    delta-t              = 0.001
> >      >    xtcprec              = 1000
> >      >    fourierspacing       = 0.12
> >      >    nkx                  = 60
> >      >    nky                  = 60
> >      >    nkz                  = 60
> >      >    pme-order            = 4
> >      >    ewald-rtol           = 1e-05
> >      >    ewald-geometry       = 0
> >      >    epsilon-surface      = 0
> >      >    optimize-fft         = FALSE
> >      >    ePBC                 = xyz
> >      >    bPeriodicMols        = FALSE
> >      >    bContinuation        = TRUE
> >      >    bShakeSOR            = FALSE
> >      >    etc                  = Nose-Hoover
> >      >    bPrintNHChains       = FALSE
> >      >    nsttcouple           = 10
> >      >    epc                  = No
> >      >    epctype              = Isotropic
> >      >    nstpcouple           = -1
> >      >    tau-p                = 1
> >      >    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}
> >      >    compress (3x3):
> >      >       compress[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> >      >       compress[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
> >      >       compress[    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
> >      >    verlet-buffer-drift  = 0.005
> >      >    rlist                = 1
> >      >    rlistlong            = 1
> >      >    nstcalclr            = 10
> >      >    rtpi                 = 0.05
> >      >    coulombtype          = PME
> >      >    coulomb-modifier     = Potential-shift
> >      >    rcoulomb-switch      = 0
> >      >    rcoulomb             = 1
> >      >    vdwtype              = Cut-off
> >      >    vdw-modifier         = Potential-shift
> >      >    rvdw-switch          = 0
> >      >    rvdw                 = 1
> >      >    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             = EnerPres
> >      >    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:      1501.9     44334.1
> >      >    ref-t:         300         300
> >      >    tau-t:         2.5         2.5
> >      > anneal:          No          No
> >      > ann-npoints:           0           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 12 OpenMP threads
> >      >
> >      > Detecting CPU-specific acceleration.
> >      > Present hardware specification:
> >      > Vendor: GenuineIntel
> >      > Brand:  Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
> >      > Family:  6  Model: 62  Stepping:  4
> >      > Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
> >      > nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
> >      > sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> >      > Acceleration most likely to fit this hardware: AVX_256
> >      > Acceleration selected at GROMACS compile time: AVX_256
> >      >
> >      > 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 0.320163 nm for Ewald
> >      > Cut-off's:   NS: 1   Coulomb: 1   LJ: 1
> >      > Long Range LJ corr.: <C6> 2.8855e-04
> >      > System total charge: 0.000
> >      > Generated table with 1000 data points for Ewald.
> >      > Tabscale = 500 points/nm
> >      > Generated table with 1000 data points for LJ6.
> >      > Tabscale = 500 points/nm
> >      > Generated table with 1000 data points for LJ12.
> >      > Tabscale = 500 points/nm
> >      > Generated table with 1000 data points for 1-4 COUL.
> >      > Tabscale = 500 points/nm
> >      > Generated table with 1000 data points for 1-4 LJ6.
> >      > Tabscale = 500 points/nm
> >      > Generated table with 1000 data points for 1-4 LJ12.
> >      > Tabscale = 500 points/nm
> >      >
> >      > Using AVX-256 4x4 non-bonded kernels
> >      >
> >      > Using Lorentz-Berthelot Lennard-Jones combination rule
> >      >
> >      > Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05
> >      > Initialized non-bonded Ewald correction tables, spacing: 6.60e-04
> >      > size: 3033
> >      >
> >      > Pinning threads with an auto-selected logical core stride of 1
> >      >
> >      > Initializing LINear Constraint Solver
> >      >
> >      > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> >      > B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> >      > LINCS: A Linear Constraint Solver for molecular simulations
> >      > J. Comp. Chem. 18 (1997) pp. 1463-1472
> >      > -------- -------- --- Thank You --- -------- --------
> >      >
> >      > The number of constraints is 292
> >      >
> >      > ++++ 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 --- -------- --------
> >      >
> >      > Center of mass motion removal mode is Linear
> >      > We have the following groups for center of mass motion removal:
> >      >   0:  rest
> >      > There are: 22765 Atoms
> >      > Initial temperature: 299.915 K
> >      >
> >      >
> >      > Am 15/07/15 um 17:57 schrieb Shirts, Michael R. (mrs5pt):
> >      >>> There I also got a linear drift (but smaller) of 0.78 kJ/mol/ps
> >      >>> (3.436*10^-5 kJ/mol/ps per atom).
> >      >>> For comparison reasons I also did a NVT Nose-Hoover Simulation with
> >      >>> manually set rlist=1.012nm: There I got a comparable linear
> >     drift of
> >      >>> 0.67
> >      >>> kJ/mol/ps (2.94*10^-5 kJ/mol/ps per atom). So no differences
> >     between
> >      >>> NVE
> >      >>> and NVT so far in my opinion...
> >      >>
> >      >> So sounds like the conserved quantity drift with NVT is not due to
> >      >> NH, but
> >      >> due to something else with the underlying dynamics.
> >      >>
> >      >> Best,
> >      >> ~~~~~~~~~~~~
> >      >> Michael Shirts
> >      >> Associate Professor
> >      >> Department of Chemical Engineering
> >      >> University of Virginia
> >      >>michael.shirts at virginia.edu  <mailto:michael.shirts at virginia.edu>
> >      >> (434) 243-1821
> >      >>
> >      >>
> >      >>
> >      >> On 7/15/15, 11:41 AM, "Bernhard"<b.reuter at uni-kassel.de
> >      <mailto:b.reuter at uni-kassel.de>> wrote:
> >      >>
> >      >>> I mean a drift of the total energy in NVE - while with
> >     Nose-Hoover the
> >      >>> drift is in the Conserved-Energy quantity of g_energy (the
> >     total energy
> >      >>> shows no drift with Noose-Hoover...).
> >      >>>
> >      >>> Am 15/07/15 um 17:38 schrieb Bernhard:
> >      >>>> I also did a NVE simulation with the same parameters, system and
> >      >>>> starting conditions but with manually set rlist=1.012nm (since
> >      >>>> verlet-buffer-drift doesnt work in NVE):
> >      >>>> There I also got a linear drift (but smaller) of 0.78 kJ/mol/ps
> >      >>>> (3.436*10^-5 kJ/mol/ps per atom).
> >      >>>> For comparison reasons I also did a NVT Nose-Hoover Simulation
> >     with
> >      >>>> manually set rlist=1.012nm:
> >      >>>> There I got a comparable linear drift of 0.67 kJ/mol/ps
> >     (2.94*10^-5
> >      >>>> kJ/mol/ps per atom).
> >      >>>> So no differences between NVE and NVT so far in my opinion...
> >      >>>>
> >      >>>>
> >      >>>>
> >      >>>> Best,
> >      >>>> Bernhard
> >      >>>>
> >      >>>> Am 15/07/15 um 17:10 schrieb Shirts, Michael R. (mrs5pt):
> >      >>>>> The conserved quantity in nose-hoover is not quite as good as the
> >      >>>>> conserved energy, which should have no drift at all.  For NH, the
> >      >>>>> conserved quantity should drift as a random Gaussian process with
> >      >>>>> mean
> >      >>>>> zero (i.e. go with sqrt(N)). It shouldn't be drifting linearly.
> >      >>>>>
> >      >>>>> I would check to see if your system conserved energy when run
> >     with
> >      >>>>> NVE
> >      >>>>> (use the endpoint of the NPT simulation).  It's easier to
> >     diagnose
> >      >>>>> any
> >      >>>>> problems with an NVE simulation, which should have virtually no
> >      >>>>> drift, vs
> >      >>>>> a NVT simulation, which has random noise drift.  Odds are, if
> >      >>>>> there is
> >      >>>>> a
> >      >>>>> problem with the NVT simulation, it will also show up in the NVE
> >      >>>>> simulation if only the thermostat is removed.
> >      >>>>>
> >      >>>>> Also, consider looking at
> >      >>>>>http://pubs.acs.org/doi/abs/10.1021/ct300688p
> >      >>>>> for tests of whether the ensemble generated is correct.
> >      >>>>>
> >      >>>>> Best,
> >      >>>>> ~~~~~~~~~~~~
> >      >>>>> Michael Shirts
> >      >>>>> Associate Professor
> >      >>>>> Department of Chemical Engineering
> >      >>>>> University of Virginia
> >      >>>>>michael.shirts at virginia.edu  <mailto:michael.shirts at virginia.edu>
> >      >>>>> (434) 243-1821
> >      >>>>>
> >      >>>>>
> >      >>>>>
> >      >>>>> On 7/15/15, 10:58 AM, "Bernhard"<b.reuter at uni-kassel.de
> >      <mailto:b.reuter at uni-kassel.de>> wrote:
> >      >>>>>
> >      >>>>>> Dear Gromacs Users and Developers,
> >      >>>>>>
> >      >>>>>> I have a problem regarding energy conservation in my 10ns NVT
> >      >>>>>> protein+water+ions (22765 atoms) production (minimization and
> >      >>>>>> equilibration for more than 15ns was carried out in NPT before)
> >      >>>>>> simulations using a Nose-Hoover thermostat (tau=2.5ps).
> >      >>>>>> On first glance everything looks fine - the potential,
> >     kinetic and
> >      >>>>>> total
> >      >>>>>> energy are nearly perfectly constant (with normal
> >     fluctuations) -
> >      >>>>>> but
> >      >>>>>> when I checked the "Conserved-Energy" quantity that g_energy
> >      >>>>>> outputs I
> >      >>>>>> had to recognize a significant (nearly perfectly) linear
> >     downward
> >      >>>>>> drift
> >      >>>>>> of this "to-be-conserved" quantity of around 1.7 kJ/mol/ps
> >      >>>>>> (7.48*10^-5
> >      >>>>>> kJ/mol/ps per atom).
> >      >>>>>> This appears somehow disturbing to me since I would expect
> >     that this
> >      >>>>>> Conserved-Energy is the conserved energy of the extended
> >     Nose-Hoover
> >      >>>>>> Hamiltonian - which should by definition be conserved.
> >      >>>>>>
> >      >>>>>> If it would be a drift caused by normal round-off error due to
> >      >>>>>> single
> >      >>>>>> precision I would expect it to grow with Sqrt(N) and not withN
> >      >>>>>> (linear)
> >      >>>>>> (N=number of steps).
> >      >>>>>> So I would like to know if this is a normal behaviour and
> >     also what
> >      >>>>>> could cause this (buffer size, precision, constraints etc)?
> >      >>>>>> Also I would like to know, if I am correct with my guess
> >     that the
> >      >>>>>> "Conserved-Energy" quantity is in this case the energy of the
> >      >>>>>> extended
> >      >>>>>> Nose-Hoover Hamiltonian?
> >      >>>>>> The .mdp file is atatched (don't be confused about rlist=1 -
> >      >>>>>> since Im
> >      >>>>>> using the Verlet-scheme the verlet-buffer-drift option
> >     should be by
> >      >>>>>> default active and determine the rlist value (Verlet
> >     buffer-size)
> >      >>>>>> automatically).
> >      >>>>>>
> >      >>>>>> Best regards,
> >      >>>>>> Bernhard
> >      >>>>>>
> >      >>>>>> ; Run parameters
> >      >>>>>> integrator    = md        ; leap-frog integrator
> >      >>>>>> nsteps        = 10000000    ; 10000 ps = 10 ns
> >      >>>>>> dt        = 0.001        ; 1 fs
> >      >>>>>> ; Output control
> >      >>>>>> nstxout        = 5000        ; save coordinates every ps
> >      >>>>>> nstvout        = 5000        ; save velocities every ps
> >      >>>>>> nstxtcout    = 1000        ; xtc compressed trajectory output
> >      >>>>>> every ps
> >      >>>>>> nstenergy    = 1000        ; save energies every ps
> >      >>>>>> nstlog        = 5000        ; update log file every ps
> >      >>>>>> ; Bond parameters
> >      >>>>>> continuation    = yes        ; continue from NPT
> >      >>>>>> constraint_algorithm = lincs    ; holonomic constraints
> >      >>>>>> constraints    = h-bonds    ; all bonds (even heavy atom-H
> >     bonds)
> >      >>>>>> constrained
> >      >>>>>> lincs_iter    = 1        ; accuracy of LINCS
> >      >>>>>> lincs_order    = 4        ; also related to accuracy
> >      >>>>>> ; Neighborsearching
> >      >>>>>> cutoff-scheme    = Verlet    ; Verlet cutoff-scheme insteadof
> >      >>>>>> group-scheme (no charge-groups used)
> >      >>>>>> ns_type        = grid        ; search neighboring grid cells
> >      >>>>>> nstlist        = 10        ; 10 fs
> >      >>>>>> rlist        = 1.0        ; short-range neighborlist cutoff
> >     (in nm)
> >      >>>>>> rcoulomb    = 1.0        ; short-range electrostatic cutoff
> >     (in nm)
> >      >>>>>> rvdw        = 1.0        ; short-range van der Waals cutoff
> >     (in nm)
> >      >>>>>> ; Electrostatics
> >      >>>>>> coulombtype    = PME        ; Particle Mesh Ewald for long-range
> >      >>>>>> electrostatics
> >      >>>>>> pme_order    = 4        ; cubic interpolation
> >      >>>>>> fourierspacing    = 0.12        ; grid spacing for FFT
> >      >>>>>> ; Temperature coupling is on
> >      >>>>>> tcoupl        = nose-hoover    ; modified Berendsen thermostat
> >      >>>>>> tc-grps        = Protein Non-Protein    ; two coupling
> >     groups - more
> >      >>>>>> accurate
> >      >>>>>> tau_t        = 2.5    2.5    ; time constant, in ps
> >      >>>>>> ref_t        = 300     300    ; reference temperature, one
> >     for each
> >      >>>>>> group, in K
> >      >>>>>> ; Pressure coupling is off
> >      >>>>>> pcoupl        = no         ; no pressure coupling in NVT
> >      >>>>>> ; Periodic boundary conditions
> >      >>>>>> pbc        = xyz        ; 3-D PBC
> >      >>>>>> ; Dispersion correction
> >      >>>>>> DispCorr    = EnerPres    ; account for cut-off vdW scheme
> >      >>>>>> ; Velocity generation
> >      >>>>>> gen_vel        = no        ; don¹t assign velocities from
> >     Maxwell
> >      >>>>>> distribution
> >      >>>>>>
> >      >>>>>> --
> >      >>>>>> Gromacs Developers mailing list
> >      >>>>>>
> >      >>>>>> * Please search the archive at
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> >      >>>>>> before
> >      >>>>>> posting!
> >      >>>>>>
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> >      >>>>>>
> >      >>>>>>
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> >      >>>>>>
> >      >>>>>> or send a mail togmx-developers-request at gromacs.org
> ><mailto:gmx-developers-request at gromacs.org>.
> >      >>> --
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> >
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> >     Gromacs Developers mailing list
> >
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> >
>
>
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
> spoel at xray.bmc.uu.se     http://folding.bmc.uu.se
> -- 
> Gromacs Developers mailing list
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