RE: [gmx-users] נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain
Berk Hess
gmx3 at hotmail.com
Wed Jul 11 10:18:56 CEST 2012
Hi,
You didn't write what your coupling groups are.
But using tau_t=0 would scale velocity to 0 in a single step and they would stay close to 0.
Cheers,
Berk
> Date: Tue, 10 Jul 2012 21:04:08 -0700
> From: InonShar at TAU.ac.IL
> To: gmx-users at gromacs.org
> Subject: [gmx-users] נושא: RE: Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain
>
> tcoupl =v-rescale
> See grompp .mdp below
> Inon Sharony
> ינון שרוני
>
> "Berk Hess [via GROMACS]" <ml-node+s5086n4999279h86 at n6.nabble.com> כתב:
>
>
> Hi,
>
> You can't have ret_t=0 with Nose-Hoover.
> We should add a check for this.
>
> Cheers,
>
> Berk
>
>
> > Date: Thu, 28 Jun 2012 11:15:15 +0300
> > From: [hidden email]
> > To: [hidden email]
> > Subject: [gmx-users] Discontinuity in first time-step velocities for diatomic molecule locally coupled to thermal drain
> >
> > Good morning.
> >
> > While doing some verification, I tried to simulate a harmonically bound
> > diatomic molecule where one of the atoms is coupled to a thermal reservoir
> > held at zero Kelvin (a thermal "drain" or "sink"). The initial conditions
> > were such that the atom coupled to the bath starts from rest and the other
> > has some initial velocity (set in conf.gro). I notice that while the
> > initial velocities are read in properly, the velocities in subsequent
> > time-steps are far smaller, and continue to fluctuate among these smaller
> > values (by small I mean a difference of two orders of magnitude, when the
> > initial velocity was 1 nm/ps). This is also visible in a sudden drop in
> > the kinetic energy and temperature immediately after the first time step.
> > The problem is that I've set COMM=None.Is there a separate mechanism which
> > subtracts velocities after the beginning of the first time-step? This does
> > not happen when there is no coupling to the thermal bath.
> >
> > Many thanks,
> >
> > --
> > Inon Sharony
> > J+N+W+N% ShR+W+N+J+
> > 972-3-6407634
> > Please consider your environmental responsibility before printing this e-mail.
> >
> > Further information:
> > ( conf.gro , topol.itp , traj.trr , energy.xvg , topol.tpr )
> >
> > conf.gro:
> >
> > Molecule starting from Minimal Potential Energy Configuration with
> > non-zero initial velocity
> > 2
> > 1SAU S 1 3.150 3.150 3.270 0.000 0.000 0.000
> > 1SAU S 2 3.150 3.150 3.030 0.000 0.000 1.000
> > 6.37511 6.37511 6.37511
> >
> > ___________________________________________________________________________
> >
> > grompp.mdp:
> >
> > integrator = md-vv-avek
> > dt = 0.001
> > nsteps = 999
> > ;
> > ;------------------------------------------------------------------------------------------------
> > nstlog = 1
> > nstcalcenergy = 1
> > ;------------------------------------------------------------------------------------------------
> > ;
> > pbc = no ; no periodic boundary conditions (only one
> > molecule)
> > comm_mode = None
> > nstcomm = 1
> > ;
> > ;------------------------------------------------------------------------------------------------
> > ; 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 1
> > ;
> > ;-------------------------------------------------------------------------------------------------
> > ; neighbor list search
> > nstype = simple ; particle (as opposed to domain)
> > decomposition
> > coulombtype = cut-off
> > ;
> > ;-------------------------------------------------------------------------------------------------
> > ;
> > ; Langevin dynamics temperature coupling
> > ;
> > ld_seed = 1 ; (1993) [integer]
> > tcoupl = v-rescale
> > nsttcouple = 1
> > ;
> > tc-grps = 0 1
> > tau_t = 1 0 ; mass/gamma [a.m.u. nanosecond]
> > ref_t = 0 0 ; reference (bath) temperature
> >
> > ;-------------------------------------------------------------------------------------------------
> > ;
> > ; Velocity generation
> > gen_vel = no ; (no)
> > gen_temp = 0 ; (300) [K]
> > gen_seed = 1 ; (-1) = from PID
> >
> > ___________________________________________________________________________
> >
> > topol.itp:
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > SAU 3
> >
> > [ atoms ]
> > ; nr type resnr resid atom cgnr charge mass
> > 1 S 1 SAU S 1 0.000 32.0600
> > 2 S 1 SAU S 2 0.000 32.0600
> >
> > [ bonds ]
> > ; ai aj fu c0, c1, ...
> > 1 2 1 0.238 680000.0 ; harmonic
> >
> > ___________________________________________________________________________
> >
> > traj.trr:
> >
> > traj.trr frame 0:
> > natoms= 2 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 (2x3):
> > x[ 0]={ 3.15000e+00, 3.15000e+00, 3.27000e+00}
> > x[ 1]={ 3.15000e+00, 3.15000e+00, 3.03000e+00}
> > v (2x3):
> > v[ 0]={ 0.00000e+00, 0.00000e+00, -2.12102e-02}
> > v[ 1]={ 0.00000e+00, 0.00000e+00, 1.02121e+00}
> > f (2x3):
> > f[ 0]={ 0.00000e+00, 0.00000e+00, -1.36000e+03}
> > f[ 1]={ 0.00000e+00, 0.00000e+00, 1.36000e+03}
> > traj.trr frame 1:
> > natoms= 2 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 (2x3):
> > x[ 0]={ 3.15000e+00, 3.15000e+00, 3.26996e+00}
> > x[ 1]={ 3.15000e+00, 3.15000e+00, 3.03002e+00}
> > v (2x3):
> > v[ 0]={ 0.00000e+00, 0.00000e+00, -6.29244e-02}
> > v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > f (2x3):
> > f[ 0]={ 0.00000e+00, 0.00000e+00, -1.31673e+03}
> > f[ 1]={ 0.00000e+00, 0.00000e+00, 1.31673e+03}
> > traj.trr frame 2:
> > natoms= 2 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 (2x3):
> > x[ 0]={ 3.15000e+00, 3.15000e+00, 3.26987e+00}
> > x[ 1]={ 3.15000e+00, 3.15000e+00, 3.03004e+00}
> > v (2x3):
> > v[ 0]={ 0.00000e+00, 0.00000e+00, -1.02810e-01}
> > v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > f (2x3):
> > f[ 0]={ 0.00000e+00, 0.00000e+00, -1.24604e+03}
> > f[ 1]={ 0.00000e+00, 0.00000e+00, 1.24604e+03}
> > .
> > .
> > .
> >
> > ___________________________________________________________________________
> >
> > energy.xvg:
> >
> > # This file was created Tue Jun 26 22:00:38 2012
> > # by the following command:
> > # g_energy_d -s -dp -quiet
> > #
> > # g_energy_d is part of G R O M A C S:
> > #
> > # Go Rough, Oppose Many Angry Chinese Serial killers
> > #
> > @ title "Gromacs Energies"
> > @ xaxis label "Time (ps)"
> > @ yaxis label "(kJ/mol), (K)"
> > @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 "Bond"
> > @ s1 legend "Potential"
> > @ s2 legend "Kinetic En."
> > @ s3 legend "Total Energy"
> > @ s4 legend "Conserved En."
> > @ s5 legend "Temperature"
> > 0.000000 1.360000000000 1.360000000000 8.033028696195
> > 9.393028696195 9.393028696195 322.048544262812
> > 0.001000 1.274838872373 1.274838872373 0.077195406901
> > 1.352034279274 17.389274589248 3.094806374580
> > 0.002000 1.141621384530 1.141621384530 0.181863160294
> > 1.323484544824 17.374836589202 7.290994249209
> > 0.003000 0.971972108898 0.971972108898 0.325139897720
> > 1.297112006618 17.361628208451 13.035037555885
> > 0.004000 0.780311882060 0.780311882060 0.493462222612
> > 1.273774104672 17.350136510882 19.783172256830
> > 0.005000 0.582583355004 0.582583355004 0.671485683506
> > 1.254069038510 17.340700175901 26.920230842567
> > 0.006000 0.394878246021 0.394878246021 0.843413133674
> > 1.238291379694 17.333484424611 33.812897001156
> > 0.007000 0.232083734770 0.232083734770 0.994330449068
> > 1.226414183837 17.328471077977 39.863255286285
> > 0.008000 0.106661122703 0.106661122703 1.111437369236
> > 1.218098491939 17.325464232219 44.558136207263
> > 0.009000 0.027656180079 0.027656180079 1.185072612382
> > 1.212728792461 17.324110715250 47.510213656278
> > 0.010000 0.000018869457 0.000018869457 1.209452000918
> > 1.209470870375 17.323933267090 48.487596768555
> > 0.011000 0.024282388081 0.024282388081 1.183064285501
> > 1.207346673582 17.324373367123 47.429698725646
> > 0.012000 0.096620173650 0.096620173650 1.108699349473
> > 1.205319523123 17.324839892590 44.448367487097
> > .
> > .
> > .
> >
> > ___________________________________________________________________________
> >
> > topol.tpr:
> >
> > inputrec:
> > integrator = md-vv-avek
> > 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 = V-rescale
> > 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 3
> > ref_t: 0 0
> > tau_t: 1 0
> > anneal: No No
> > ann_npoints: 0 0
> > acc: 0 0 0
> > nfreeze: N N N
> > energygrp_flags[ 0]: 0 0
> > energygrp_flags[ 1]: 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 = 2
> > lambda = 0.000000e+00
> > topology:
> > name="Free Sulfur Molecule"
> > #atoms = 2
> > molblock (0):
> > moltype = 0 "SAU"
> > #molecules = 1
> > #atoms_mol = 2
> > #posres_xA = 0
> > #posres_xB = 0
> > ffparams:
> > atnr=1
> > ntypes=2
> > functype[0]=LJ_SR, c6= 9.98400640e-03, c12= 1.30754560e-05
> > functype[1]=BONDS, b0A= 2.38000e-01, cbA= 6.80000e+05, b0B=
> > 2.38000e-01, cbB= 6.80000e+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="SAU"
> > atoms:
> > atom (2):
> > 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]={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 (2):
> > atom[0]={name="S"}
> > atom[1]={name="S"}
> > type (2):
> > type[0]={name="S",nameB="S"}
> > type[1]={name="S",nameB="S"}
> > residue (1):
> > residue[0]={name="SAU", nr=1, ic=' '}
> > cgs:
> > nr=2
> > cgs[0]={0..0}
> > cgs[1]={1..1}
> > excls:
> > nr=2
> > nra=4
> > excls[0][0..1]={0, 1}
> > excls[1][2..3]={0, 1}
> > Bond:
> > nr: 3
> > iatoms:
> > 0 type=1 (BONDS) 0 1
> > grp[T-Coupling ] nr=2, name=[ 0 1]
> > grp[Energy Mon. ] nr=2, name=[ 0 1]
> > 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 (6):
> > grpname[0]={name="System"}
> > grpname[1]={name="Other"}
> > grpname[2]={name="SAU"}
> > grpname[3]={name="0"}
> > grpname[4]={name="1"}
> > grpname[5]={name="rest"}
> > groups T-Cou Energ Accel Freez User1 User2 VCM XTC Or. R
> > QMMM
> > allocated 2 2 0 0 0 0 0 0
> > 0 0
> > groupnr[ 0] = 0 0 0 0 0 0 0 0
> > 0 0
> > groupnr[ 1] = 1 1 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 (2x3):
> > x[ 0]={ 3.15000e+00, 3.15000e+00, 3.27000e+00}
> > x[ 1]={ 3.15000e+00, 3.15000e+00, 3.03000e+00}
> > v (2x3):
> > v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > v[ 1]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
> > Group statistics
> > T-Coupling : 1 1 (total 2 atoms)
> > Energy Mon. : 1 1 (total 2 atoms)
> > Acceleration: 2 (total 2 atoms)
> > Freeze : 2 (total 2 atoms)
> > User1 : 2 (total 2 atoms)
> > User2 : 2 (total 2 atoms)
> > VCM : 2 (total 2 atoms)
> > XTC : 2 (total 2 atoms)
> > Or. Res. Fit: 2 (total 2 atoms)
> > QMMM : 2 (total 2 atoms)
> > --
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