Dear all,
a similar problem was proposed in this list in 2002: http://www.gromacs.org/pipermail/gmx-users/2002-August/002339.html I cannot solve my problem, when testing tip5p in gromacs. T( c) density((g/cm^3) -E(kcal/mol) REF1 25.0 0.999 9.8676 REF2 25.0 0.984 9.682 my results 25.0 0.984 -7.907 (data published (REF1:JCP 112, p8910 (2000)), REF2: J. Chem. Phys. 117(19):8892-8897. (2002)) ) I want to what results in the big difference above. my main parameters: a. 512 water molecules in NVT system from 1ns average collections after 1ns equilibrium. integrator = md dt = 0.001 nstlist = 10 ns_type = grid pbc = xyz rlist = 1 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.22 DispCorr = Ener ; fourierspacing = 0.12 pme_order = 6 Tcoupl = Berendsen tau_t = 0.5 ref_t = 298 Thanks a lot in advance! Yusong ////////////////////////////////////////////////////////////////////////// PS: here is md0.log: CPU= 0, lastcg= 127, targetcg= 383, myshift= 2 CPU= 1, lastcg= 255, targetcg= 511, myshift= 2 CPU= 2, lastcg= 383, targetcg= 128, myshift= 2 CPU= 3, lastcg= 511, targetcg= 256, myshift= 2 nsb->shift = 2, nsb->bshift= 0 Listing Scalars nsb->nodeid: 0 nsb->nnodes: 4 nsb->cgtotal: 512 nsb->natoms: 2560 nsb->shift: 2 nsb->bshift: 0 Nodeid index homenr cgload workload 0 0 640 128 128 1 640 640 256 256 2 1280 640 384 384 3 1920 640 512 512 parameters of the run: integrator = md nsteps = 1000000 init_step = 0 ns_type = Grid nstlist = 10 ndelta = 2 bDomDecomp = FALSE decomp_dir = 0 nstcomm = 1 comm_mode = Linear nstcheckpoint = 1000 nstlog = 1500 nstxout = 250 nstvout = 250 nstfout = 250 nstenergy = 250 nstxtcout = 1000 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 24 nky = 24 nkz = 21 pme_order = 6 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bUncStart = FALSE bShakeSOR = FALSE etc = Berendsen epc = No epctype = Isotropic 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} andersen_seed = 815131 rlist = 1 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1 vdwtype = Cut-off rvdw_switch = 0 rvdw = 1.22 epsilon_r = 1 epsilon_rf = 1 tabext = 1 gb_algorithm = Still nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 implicit_solvent = No DispCorr = Ener fudgeQQ = 0.5 free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 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 dihre-tau = 0 nstdihreout = 100 em_stepsize = 0.01 em_tol = 10 niter = 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr = 10 ConstAlg = Lincs shake_tol = 1e-04 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} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 userreal1 = 0 userreal2 = 0 userreal3 = 0 userreal4 = 0 grpopts: nrdf: 3069 ref_t: 298 tau_t: 0.5 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 Max number of connections per atom is 4 Total number of connections is 1536 Max number of graph edges per atom is 4 Total number of graph edges is 1024 Table routines are used for coulomb: TRUE Table routines are used for vdw: FALSE Using a Gaussian width (1/beta) of 0.320163 nm for Ewald Cut-off's: NS: 1 Coulomb: 1 LJ: 1.22 System total charge: 0.000 Generated table with 1110 data points for Ewald. Tabscale = 500 points/nm Generated table with 1110 data points for LJ6. Tabscale = 500 points/nm Generated table with 1110 data points for LJ12. Tabscale = 500 points/nm Will do PME sum in reciprocal space. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essman, L. Perela, 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 --- -------- -------- Parallelized PME sum used. PARALLEL FFT DATA: local_nx: 6 local_x_start: 0 local_ny_after_transpose: 6 local_y_start_after_transpose 0 Removing pbc first time Done rmpbc Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: System, initial mass: 9223.92 There are: 384 Atoms There are: 256 VSites --- P.O.800-204 Haiping Fang Group Shanghai Institute of Applied Physics Chinese Academy of Sciences, China (201800) Send email to: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] Tel: (int : +86 21 59554533), (loc : 21 59554533)
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