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: inons...@tau.ac.il > To: gmx-users@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+s5086n4999279...@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) > > -- > > gmx-users mailing list [hidden email] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Only plain text messages are allowed! > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [hidden email]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list [hidden email] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [hidden email]. > * Can't post? 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