[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
> > >>>>>>
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> > >>>>>>
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> ><mailto:gmx-developers-request at gromacs.org>.
> > >>> --
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> >http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
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> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> > >>> or send a mail togmx-developers-request at gromacs.org
> ><mailto:gmx-developers-request at gromacs.org>.
> > >
> >
> > --
> > Gromacs Developers mailing list
> >
> > * Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List
> > before posting!
> >
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> > or send a mail togmx-developers-request at gromacs.org
> ><mailto:gmx-developers-request at gromacs.org>.
> >
> >
> >
>
>
> --
> 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
>
> * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before posting!
>
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>
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>
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