[gmx-users] error (full of nan)
Herbert Georg
hcgeorg at if.usp.br
Fri Feb 27 20:07:01 CET 2004
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:
;
; 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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