[gmx-users] error (full of nan)
David
spoel at xray.bmc.uu.se
Fri Feb 27 21:28:00 CET 2004
On Fri, 2004-02-27 at 19:37, Herbert Georg wrote:
> Hi, I'm new to gromacs.
> I'm trying to perform a simulation of 1 water molecule at 50K with no
> periodic boundary conditions.
> But I got lots of NAN as energies and temperatures. What am I doing wrong??
> Here is my md.mdp file:
this model has a bond potential with a singularity, i.e. energy goes to
-infinity when the bond is too long.
>
> ;
> ; Input file
> ;
> title = agua gasosa ; a string
> cpp = /lib/cpp ; c-preprocessor
> integrator = md
> dt = 0.00025 ; time step
> nsteps = 200000 ; number of steps
> comm_mode = Angular ; mode of com reset
> nstcomm = 1 ; reset c.o.m. motion
> nstxout = 2000 ; write coords
> nstvout = 20000 ; write velocities
> nstlog = 1000 ; print to logfile
> nstenergy = 2000 ; print energies
> nstlist = 0 ; update pairlist
> pbc = no ; box replication
> rlist = 0.0 ; cut-off for ns
> rvdw = 0.0 ; cut-off for vdw
> rcoulomb = 0.0 ; cut-off for coulomb
> Tcoupl = berendsen ; temperature coupling
> tc_grps = System
> ref_t = 50
> tau_t = 0.1
> Pcoupl = no ; pressure bath
> gen_vel = yes ; generate initial
> velocities
> gen_temp = 50 ; initial temperature
> gen_seed = -1 ; random seed
> constraints = none ; fully flexible
>
>
>
> And here is my topology file:
>
>
> #include <flexwat-ferguson.itp>
>
> [ system ]
> 1 water molecule
>
> [ molecules ]
> SOL 1
>
>
>
>
> And here is my md.log file:
>
>
>
>
> :-) G R O M A C S (-:
>
> Good gRace! Old Maple Actually Chews Slate
>
> :-) VERSION 3.2 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2004, The GROMACS development team,
> check out http://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 General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) mdrun (double precision) (-:
>
>
> ++++++++ PLEASE 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 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 --- -------- --------
>
> There are 0 atoms for free energy perturbation
> Input Parameters:
> integrator = md
> nsteps = 200000
> init_step = 0
> ns_type = Simple
> nstlist = 0
> ndelta = 2
> bDomDecomp = FALSE
> decomp_dir = 0
> nstcomm = -1
> nstcheckpoint = 1000
> nstlog = 1000
> nstxout = 2000
> nstvout = 20000
> nstfout = 0
> nstenergy = 2000
> nstxtcout = 0
> init_t = 0
> delta_t = 0.00025
> 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
> 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 = 0
> coulombtype = Cut-off
> rcoulomb_switch = 0
> rcoulomb = 0
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 0
> epsilon_r = 1
> tabext = 1
> gb_algorithm = Still
> nstgbradii = 1
> rgbradii = 2
> gb_saltconc = 0
> implicit_solvent = No
> DispCorr = No
> fudgeQQ = 1
> free_energy = no
> init_lambda = 0
> sc_alpha = 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 = 0.0001
> lincs_order = 4
> lincs_warnangle = 30
> lincs_iter = 1
> bd_temp = 300
> bd_fric = 0
> ld_seed = 1993
> cos_accel = 0
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
> grpopts:
> nrdf: 3
> ref_t: 50
> tau_t: 0.1
> anneal: No
> ann_npoints: 0
> acc: 0 0 0
> nfreeze: N N N
> energygrp_excl[ 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
> CPU= 0, lastcg= 0, targetcg= 0, myshift= 0
> nsb->shift = 1, nsb->bshift= 0
> Neighbor Search Blocks
> nsb->nodeid: 0
> nsb->nnodes: 1
> nsb->cgtotal: 1
> nsb->natoms: 3
> nsb->shift: 1
> nsb->bshift: 0
> Nodeid index homenr cgload workload
> 0 0 3 1 1
>
> Max number of graph edges per atom is 2
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw: FALSE
> Cut-off's: NS: 0 Coulomb: 0 LJ: 0
> Generated table with 2000 data points for COUL.
> Tabscale = 2000 points/nm
> Generated table with 2000 data points for LJ6.
> Tabscale = 2000 points/nm
> Generated table with 2000 data points for LJ12.
> Tabscale = 2000 points/nm
> Going to determine what solvent types we have.
> There are 1 molecules, 1 charge groups and 3 atoms
> There are 0 optimized solvent molecules on node 0
> There are 1 optimized water molecules on node 0
> Center of mass motion removal mode is Angular
> We have the following groups for center of mass motion removal:
> 0: rest, initial mass: 18.0154
> There are: 3 Atom
> Started mdrun on node 0 Fri Feb 27 15:32:01 2004
> Initial temperature: 147.727 K
> Step Time Lambda
> 0 0.00000 0.00000
>
>
> Testing x86 processor CPUID...
> CPU manufactured by AMD.
>
> Testing x86 SSE2 capabilities...
> No SSE2 support found for this CPU.
>
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
> -------- -------- --- Thank You --- -------- --------
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> -4.45478e+06 2.31723e+00 0.00000e+00 0.00000e+00 -4.45478e+06
> Kinetic En. Total Energy Temperature Pressure (bar)
> 1.03288e+06 -3.42190e+06 8.28172e+07 0.00000e+00
>
> Large VCM(group rest): -0.06060, 238.90671, -1301.10905,
> ekin-cm: 1.57631e+07
> Group rest with mass 1.80154e+01, Ekrot 2.89714e+07 Det(I) = 2.91221e+75
> COM: -0.00001 0.15850 -0.34096
> P: -1.09180 4304.00000 -23440.00000
> V: -0.06060 238.90671 -1301.10905
> J: -316610753315915956224.00000 33312703967920128.00000
> 1642434040659967.75000
> w: -0.00000 0.00000 0.00000
> Inertia tensor (3x3):
> Inertia tensor[ 0]={ 1.63743e+25, 8.63791e+28, -6.46686e+28}
> Inertia tensor[ 1]={ 8.63791e+28, 5.81909e+32, -5.44967e+30}
> Inertia tensor[ 2]={-6.46686e+28, -5.44967e+30, 1.14811e+33}
> Large VCM(group rest):
> 586338543056364270781820368748131027312759306679389061647765058748856825227886380049817667633152.00000,
> 2422510025752191784457263020949323022252851630819615166183369881592818127533860155379926733785399296.00000,
> -3759917675051561681178909343742465903393566354268843224355025389267614366072528958726210507803459584.00000,
> ekin-cm: 1.80204e+200
> Group rest with mass 1.80154e+01, Ekrot 1.15304e+200 Det(I) = -inf
> COM:
> 252263466989477814952341030174941380533519730491739137847624224728756399323368476250671677440.00000
> 263991287158078721609561546342526966564646800733791164234201137274649339782577519083763697451008.00000
> 2422235845327634385777760938723813729230771830306887383792938704370308999602606362471760639557632.00000
> P:
> 10563123388577625641844130781291613191746187208216884401378729201183320987649573970035429695553536.00000
> 43642487117936034803495083500456288805562458800791129395557954131023593437150047718069161360288120832.00000
> -67736420883123900532910928346048836658280965812974172640560583467258231943955673122328173700932698112.00000
> V:
> 586338543056364270781820368748131027312759306679389061647765058748856825227886380049817667633152.00000
> 2422510025752191784457263020949323022252851630819615166183369881592818127533860155379926733785399296.00000
> -3759917675051561681178909343742465903393566354268843224355025389267614366072528958726210507803459584.00000
> J:
> 4785929463858546774061420167007559181287210355917049994396252801157486473335229929793964392640916749902973551833079547419627603054390149856213076890378712160504864153829851430880927578003334180525107050204048130048.00000
> -2287923500231010397007134064530571297584479540228701277641690148535589833906376418279498105963100486763799504823567782932364658788962993665495652220589321433259379274748113238427877163590187587217803948563890176.00000
> -2226438761569374338214667290811570263939157308032516593112078997054805828532035935877831467907731450843856971506177544675648904995720577183590210994111785410027994109325437405326296213466429623323285639233798144.00000
> w: 0.00000 -0.00000 -0.00000
> Inertia tensor (3x3):
> Inertia tensor[ 0]={8.45240e+218, 4.21292e+222, -3.99225e+222}
> Inertia tensor[ 1]={4.21292e+222, 2.83661e+226, -3.05784e+224}
> Inertia tensor[ 2]={-3.99225e+222, -3.05784e+224, 7.09590e+226}
> Step Time Lambda
> 1000 0.25000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 2000 0.50000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 3000 0.75000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 4000 1.00000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 5000 1.25000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 6000 1.50000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 7000 1.75000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 8000 2.00000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 9000 2.25000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 10000 2.50000 0.00000
>
> Energies (kJ/mol)
> Cubic Bonds Angle LJ (SR) Coulomb (SR) Potential
> nan nan 0.00000e+00 0.00000e+00 nan
> Kinetic En. Total Energy Temperature Pressure (bar)
> nan nan nan 0.00000e+00
>
> Step Time Lambda
> 11000 2.75000 0.00000
>
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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