Hello, I'm trying to simulate a water box with protein and drug. Having set up the simulation, starting mdrun causes no problems on its own. However, after setting the GMX_NB_GENERIC environment variable and restarting the simulation, it crashes at step 20 with too many LINCS warnings. Disabeling the environment variable makes mdrun run normal again.
Where is this different behavior coming from and is this solvable? Using Gromacs 4.0.5. Attached the screen output and the log file. Thanks in advance, Pieter van 't Hof Graduate student Utrecht University
GMX log
Description: Binary data
Log file opened on Tue Jan 12 12:05:29 2010
Host: docktop pid: 3952 nodeid: 0 nnodes: 1
The Gromacs distribution was built Thu Sep 17 14:15:57 UTC 2009 by
bui...@vernadsky (Linux 2.6.24-23-server i686)
:-) G R O M A C S (-:
GRowing Old MAkes el Chrono Sweat
:-) VERSION 4.0.5 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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 (-:
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------
++++ PLEASE READ AND 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 READ AND 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 --- -------- --------
Input Parameters:
integrator = md
nsteps = 50000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 500
nstxout = 200000
nstvout = 200000
nstfout = 0
nstenergy = 500
nstxtcout = 500
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 10
nky = 10
nkz = 10
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Parrinello-Rahman
epctype = Isotropic
tau_p = 1.5
ref_p (3x3):
ref_p[ 0]={ 1.00000e-07, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e-07, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e-07}
compress (3x3):
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
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 = 1.4
rtpi = 0.05
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 1.4
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1.4
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
sa_surface_tension = 2.092
DispCorr = No
free_energy = no
init_lambda = 0.35
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0.00065
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 = Equal
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 1.25
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 0.001
niter = 100
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 8
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: 5489.65 65.9958 42129.3
ref_t: 300 300 300
tau_t: 0.1 0.1 0.1
anneal: No No No
ann_npoints: 0 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0 0 0
energygrp_flags[ 1]: 0 0 0
energygrp_flags[ 2]: 0 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
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 1.4 Coulomb: 1.4 LJ: 1.4
System total charge: -5.000
Generated table with 1200 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1200 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Enabling SPC water optimization for 7022 molecules.
Found environment variable GMX_NB_GENERIC.
Disabling all interaction-specific nonbonded kernels.
Removing pbc first time
Initializing LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------
The number of constraints is 2838
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
++++ PLEASE READ AND 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 --- -------- --------
There are: 23864 Atoms
Max number of connections per atom is 28
Total number of connections is 69095
Max number of graph edges per atom is 4
Total number of graph edges is 33764
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 4.38e-06
Initial temperature: 299.565 K
Started mdrun on node 0 Tue Jan 12 12:05:30 2010
Step Time Lambda
0 0.00000 0.00000
Grid: 9 x 11 x 9 cells
Energies (kJ/mol)
G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
1.98224e+03 1.29360e+03 6.18462e+02 1.19765e+02 4.19147e+04
LJ (SR) Coulomb (SR) Position Rest. Potential Kinetic En.
4.13001e+04 1.20063e+08 8.94156e-01 1.20150e+08 6.70925e+04
Total Energy Temperature Pressure (bar) Cons. rmsd ()
1.20217e+08 3.38443e+02 2.64114e+06 7.82510e-06
Step 5 Warning: Pressure scaling more than 1%.
Step 6 Warning: Pressure scaling more than 1%.
Step 7 Warning: Pressure scaling more than 1%.
Step 8 Warning: Pressure scaling more than 1%.
Step 9 Warning: Pressure scaling more than 1%.
Step 10 Warning: Pressure scaling more than 1%.
Step 11 Warning: Pressure scaling more than 1%.
Step 12 Warning: Pressure scaling more than 1%.
Step 13 Warning: Pressure scaling more than 1%.
Step 14 Warning: Pressure scaling more than 1%.
Step 15 Warning: Pressure scaling more than 1%.
Step 16 Warning: Pressure scaling more than 1%.
Step 17 Warning: Pressure scaling more than 1%.
Step 18 Warning: Pressure scaling more than 1%.
Step 19 Warning: Pressure scaling more than 1%.
Step 20 Warning: Pressure scaling more than 1%.
Step 21 Warning: Pressure scaling more than 1%.
-------------------------------------------------------
Program mdrun, VERSION 4.0.5
Source code file: ../../../../src/mdlib/constr.c, line: 136
Fatal error:
Too many LINCS warnings (1576)
If you know what you are doing you can adjust the lincs warning threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
-------------------------------------------------------
"Sometimes Life is Obscene" (Black Crowes)
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