[gmx-users] Nose-Hoover does not couple

[Berk Hess]

Hi,

This is the same issue as in your other mail: ref_t should be > 0.

Cheers,

Berk

----------------------------------------
> Date: Tue, 3 Jul 2012 17:38:37 +0300
> From: InonShar at TAU.ac.IL
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Nose-Hoover does not couple
>
> I'm performing a verification of the energy dissipation of a single atom,
> thermally coupled to a heat drain (or sink). In other words, the Langevin
> equation of motion is d/dt v(t) = - gamma * v(t).
> If using the Stochastic Dynamics integrator I do indeed get dissipation,
> however if using the Nose-Hoover thermostat with either the leap-frog or
> velocity Verlet integrators the energy does not seem to dissipate. I get
> the same thing for two harmonically-bound atoms. Could anyone please take
> a look and tell me why this is?
> Also, the "Conserved Energy" I get is "not a number". I don't know what
> this means, either.
>
> energy.xvg:
>
> @ title "Gromacs Energies"
> @ xaxis label "Time (ps)"
> @ yaxis label "(kJ/mol), (K), (bar)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "LJ (SR)"
> @ s1 legend "Kinetic En."
> @ s2 legend "Total Energy"
> @ s3 legend "Conserved En."
> @ s4 legend "Temperature"
> @ s5 legend "Pressure"
> 0.000000 0.000000000000 16.030000000000
> 16.030000000000 nan 1285.303055615475 0.000000000000
> 0.001000 0.000000000000 16.030000000000
> 16.030000000000 nan 1285.303055615475 0.000000000000
> 0.002000 0.000000000000 16.030000000000
> 16.030000000000 nan 1285.303055615475 0.000000000000
> .
> .
> .
> 0.998000 0.000000000000 16.030000000000
> 16.030000000000 nan 1285.303055615475 0.000000000000
> 0.999000 0.000000000000 16.030000000000
> 16.030000000000 nan 1285.303055615475 0.000000000000
>
> =============================================
>
> Supporting files:
>
> traj.trr:
>
> traj-tss.trr frame 0:
> natoms= 1 step= 0 time=0.0000000e+00 lambda=
> 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> x (1x3):
> x[ 0]={ 3.15000e+00, 3.15000e+00, 3.15000e+00}
> v (1x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> f (1x3):
> f[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> traj-tss.trr frame 1:
> natoms= 1 step= 1 time=1.0000000e-03 lambda=
> 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> x (1x3):
> x[ 0]={ 3.15000e+00, 3.15000e+00, 3.15100e+00}
> v (1x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> f (1x3):
> f[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> traj-tss.trr frame 2:
> natoms= 1 step= 2 time=2.0000000e-03 lambda=
> 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> x (1x3):
> x[ 0]={ 3.15000e+00, 3.15000e+00, 3.15200e+00}
> v (1x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> f (1x3):
> f[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>
> .
> .
> .
>
> traj-tss.trr frame 998:
> natoms= 1 step= 998 time=9.9800000e-01 lambda=
> 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> x (1x3):
> x[ 0]={ 3.15000e+00, 3.15000e+00, 4.14800e+00}
> v (1x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> f (1x3):
> f[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> traj-tss.trr frame 999:
> natoms= 1 step= 999 time=9.9900000e-01 lambda=
> 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> x (1x3):
> x[ 0]={ 3.15000e+00, 3.15000e+00, 4.14900e+00}
> v (1x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> f (1x3):
> f[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
>
> =============================================
>
> conf.gro:
>
> Single Sulfur Atom
> 1
> 1ATM S 1 3.150 3.150 3.150 0.000 0.000 1.000
> 6.37511 6.37511 6.37511
>
> =============================================
>
> topol.itp:
>
> [ moleculetype ]
> ; Name nrexcl
> ATM 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 S 1 ATM S 1 0.000 32.0600
>
> =============================================
>
> grompp.mdp:
>
> integrator = md
> dt = 0.001
> nsteps = 999
> ;
> ;------------------------------------------------------------------------------------------------
> nstlog = 1
> nstcalcenergy = 1
> ;------------------------------------------------------------------------------------------------
> ;
> pbc = no ; no periodic boundary conditions (only one
> molecule)
> comm_mode = None ;"Angular" = remove center of mass
> translatory AND rotational motion
> nstcomm = 1 ; number of steps between removal of center
> of mass motion
> ;
> ;------------------------------------------------------------------------------------------------
> ; number of steps between writing out of different phase data and
> energetics
> nstxout = 1
> nstvout = 1
> nstfout = 1
> nstenergy = 1
> ; groups to write energetics of
> energygrps = 0
> ;
> ;-------------------------------------------------------------------------------------------------
> ; neighbor list search
> nstype = simple ; particle (as opposed to domain)
> decompositon
> coulombtype = cut-off
> ;
> ;-------------------------------------------------------------------------------------------------
> ;
> ; Langevin dynamics temperature coupling
> ;
> ld_seed = 1 ; (1993) [integer]
> tcoupl = nose-hoover
> nsttcouple = 1
> ;
> tc-grps = 0
> tau_t = 1 ; mass/gamma [a.m.u. nanosecond]
> ref_t = 0 ; reference (bath) temperature
>
> ;-------------------------------------------------------------------------------------------------
> ;
> ; Velocity generation
> gen_vel = no ; (no)
> gen_temp = 0 ; (300) [K]
> gen_seed = 1 ; (-1) = from PID
>
> =============================================
>
> topol-tss.tpr:
>
> inputrec:
> integrator = md
> nsteps = 999
> init_step = 0
> ns_type = Simple
> nstlist = 10
> ndelta = 2
> nstcomm = 0
> comm_mode = None
> nstlog = 1
> nstxout = 1
> nstvout = 1
> nstfout = 1
> nstcalcenergy = 1
> nstenergy = 1
> nstxtcout = 0
> init_t = 0
> delta_t = 0.001
> xtcprec = 1000
> nkx = 0
> nky = 0
> nkz = 0
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = no
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = Nose-Hoover
> nsttcouple = 1
> 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
> andersen_seed = 815131
> rlist = 1
> rlistlong = 1
> rtpi = 0.05
> coulombtype = Cut-off
> rcoulomb_switch = 0
> rcoulomb = 1
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1
> epsilon_r = 1
> epsilon_rf = 1
> 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
> free_energy = no
> init_lambda = 0
> delta_lambda = 0
> n_foreign_lambda = 0
> sc_alpha = 0
> sc_power = 0
> sc_sigma = 0.3
> sc_sigma_min = 0.3
> nstdhdl = 10
> separate_dhdl_file = yes
> dhdl_derivatives = yes
> dh_hist_size = 0
> dh_hist_spacing = 0.1
> 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
> 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 = 1000
> 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 = 1
> 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}
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 3
> ref_t: 0
> tau_t: 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
> header:
> bIr = present
> bBox = present
> bTop = present
> bX = present
> bV = present
> bF = not present
> natoms = 1
> lambda = 0.000000e+00
> topology:
> name="Single Sulfur Atom"
> #atoms = 1
> molblock (0):
> moltype = 0 "ATM"
> #molecules = 1
> #atoms_mol = 1
> #posres_xA = 0
> #posres_xB = 0
> ffparams:
> atnr=1
> ntypes=1
> functype[0]=LJ_SR, c6= 9.98400640e-03, c12= 1.30754560e-05
> reppow = 12
> fudgeQQ = 1
> cmap
> atomtypes:
> atomtype[ 0]={radius=-1.00000e+00, volume=-1.00000e+00,
> gb_radius=-1.00000e+00, surftens=-1.00000e+00, atomnumber= 16,
> S_hct=-1.00000e+00)}
> moltype (0):
> name="ATM"
> atoms:
> atom (1):
> atom[ 0]={type= 0, typeB= 0, ptype= Atom, m=
> 3.20600e+01, q= 0.00000e+00, mB= 3.20600e+01, qB= 0.00000e+00, resind=
> 0, atomnumber= 16}
> atom (1):
> atom[0]={name="S"}
> type (1):
> type[0]={name="S",nameB="S"}
> residue (1):
> residue[0]={name="ATM", nr=1, ic=' '}
> cgs:
> nr=1
> cgs[0]={0..0}
> excls:
> nr=1
> nra=1
> excls[0][0..0]={0}
> grp[T-Coupling ] nr=1, name=[ 0]
> grp[Energy Mon. ] nr=1, name=[ 0]
> grp[Acceleration] nr=1, name=[ rest]
> grp[Freeze ] nr=1, name=[ rest]
> grp[User1 ] nr=1, name=[ rest]
> grp[User2 ] nr=1, name=[ rest]
> grp[VCM ] nr=1, name=[ rest]
> grp[XTC ] nr=1, name=[ rest]
> grp[Or. Res. Fit] nr=1, name=[ rest]
> grp[QMMM ] nr=1, name=[ rest]
> grpname (5):
> grpname[0]={name="System"}
> grpname[1]={name="Other"}
> grpname[2]={name="ATM"}
> grpname[3]={name="0"}
> grpname[4]={name="rest"}
> groups T-Cou Energ Accel Freez User1 User2 VCM XTC Or. R
> QMMM
> allocated 0 0 0 0 0 0 0 0
> 0 0
> groupnr[ *] = 0 0 0 0 0 0 0 0
> 0 0
> box (3x3):
> box[ 0]={ 6.37511e+00, 0.00000e+00, 0.00000e+00}
> box[ 1]={ 0.00000e+00, 6.37511e+00, 0.00000e+00}
> box[ 2]={ 0.00000e+00, 0.00000e+00, 6.37511e+00}
> box_rel (3x3):
> box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> boxv (3x3):
> boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> pres_prev (3x3):
> pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> svir_prev (3x3):
> svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> fvir_prev (3x3):
> fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> nosehoover_xi: not available
> x (1x3):
> x[ 0]={ 3.15000e+00, 3.15000e+00, 3.15000e+00}
> v (1x3):
> v[ 0]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> Group statistics
> T-Coupling : 1 (total 1 atoms)
> Energy Mon. : 1 (total 1 atoms)
> Acceleration: 1 (total 1 atoms)
> Freeze : 1 (total 1 atoms)
> User1 : 1 (total 1 atoms)
> User2 : 1 (total 1 atoms)
> VCM : 1 (total 1 atoms)
> XTC : 1 (total 1 atoms)
> Or. Res. Fit: 1 (total 1 atoms)
> QMMM : 1 (total 1 atoms)
>
> --
> Inon Sharony
> J+N+W+N% ShR+W+N+J+
> 972-3-6407634
> Please consider your environmental responsibility before printing this e-mail.
> --
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