this log?
Log file opened: nodeid 0, nnodes = 1, host = unknown, process = 2964
Gromacs is Copyright (c) 1991-2003, University of Groningen, The Netherlands
This inclusion of Gromacs code in the Folding@Home Core is under
a special license (see http://folding.stanford.edu/gromacs.html)
specially granted to Stanford by the copyright holders. If you
are interested in using Gromacs, visit www.gromacs.org where
you can download a free version of Gromacs under
the terms of the GNU General Public License (GPL) as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any later version.
++++++++ 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 = sd
nsteps = 5000000
ns_type = Grid
nstlist = 10
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
nstlog = 25000
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 25000
nstxtcout = 25000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-005
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bUncStart = TRUE
bShakeSOR = FALSE
etc = No
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
ref_p[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
ref_p[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
compress (3x3):
compress[ 0]={0.00000e+000, 0.00000e+000, 0.00000e+000}
compress[ 1]={0.00000e+000, 0.00000e+000, 0.00000e+000}
compress[ 2]={0.00000e+000, 0.00000e+000, 0.00000e+000}
bSimAnn = FALSE
zero_temp_time = 0
rlist = 0.8
coulombtype = User
rcoulomb_switch = 0
rcoulomb = 4
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
DispCorr = No
fudgeQQ = 0.8333
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
em_stepsize = 0.01
em_tol = 100
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
ConstAlg = Lincs
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
bd_temp = 300
bd_fric = 0
ld_seed = 213238058
cos_accel = 0
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
solvent-model = Explicit
sasa = None
nstsasa = 1
rsasa = 0
epsilon_dd = 1
nstsasaout = 1
grpopts:
nrdf: 4349.42 707.58
ref_t: 300 300
tau_t: 1 1
acc: 0 0 0
nfreeze: N N N
energygrp_excl[ 0]: 0 0
energygrp_excl[ 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
CPU= 0, lastcg= 2543, targetcg= 1272, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 2544
nsb->natoms: 2544
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 2544 2544 2544
Max number of graph edges per atom is 14
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.8 Coulomb: 4 LJ: 1
Read user tables from 1.xvg with 2501 data points.
Tabscale = 500 points/nm
Generated table with 2500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 2500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 4 molecules, 2544 charge groups and 2544 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 18132.2
There are: 2544 Atom
Removing pbc first time
Done rmpbc
Started mdrun on node 0 Tue Apr 04 07:07:15 2006
Initial temperature: 297.954 K
starting mdrun 'p2052_abeta_4mer'
5000000 steps, 10000.0 ps.
Grid: 7 x 7 x 7 cells
Checking SSE first.
Testing x86 processor CPUID...
Testing x86 SSE capabilities...
CPU and OS support SSE.
Using Gromacs SSE single precision assembly innerloops.
Step Time Lambda Annealing
0 0.00000 0.00000 1.00000
There are 2544 atoms in your xtc output selection
++++++++ PLEASE 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 --- -------- --------
Initializing LINear Constraint Solver
number of constraints is 2572
average number of constraints coupled to one constraint is 3.6
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.136514 398 399 0.008462
After LINCS 0.000113 2460 2462 0.000029
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.001941 1873 1876 0.000415
After LINCS 0.000053 2185 2197 0.000013
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
6.00740e+003 2.89644e+002 2.21501e+003 2.59978e+003 5.40186e+003
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Potential
-3.35642e+003 -2.36558e+002 -1.55195e+004 8.98873e+001 -2.50889e+003
Kinetic En. Total Energy Temperature Pressure (bar)
6.07607e+003 3.56718e+003 2.89017e+002 2.38027e+000
Step Time Lambda Annealing
25000 50.00000 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.107943 398 399 0.008139
After LINCS 0.000128 1188 1190 0.000027
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.001969 2243 2244 0.000414
After LINCS 0.000040 1188 1190 0.000012
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
6.10245e+003 3.57640e+002 2.37282e+003 2.62954e+003 5.49219e+003
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Potential
-3.41084e+003 -2.37597e+002 -1.54689e+004 5.25166e+001 -2.11021e+003
Kinetic En. Total Energy Temperature Pressure (bar)
6.10874e+003 3.99852e+003 2.90571e+002 1.38025e+001
Step Time Lambda Annealing
50000 100.00001 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.108557 1034 1035 0.008061
After LINCS 0.000098 1561 1563 0.000029
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.002050 144 145 0.000409
After LINCS 0.000045 925 927 0.000013
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
6.12586e+003 3.35311e+002 2.38000e+003 2.57500e+003 5.42822e+003
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Potential
-3.45115e+003 -2.37805e+002 -1.55631e+004 1.43210e+002 -2.26441e+003
Kinetic En. Total Energy Temperature Pressure (bar)
6.15299e+003 3.88858e+003 2.92676e+002 -6.65865e+000
Step Time Lambda Annealing
75000 150.00000 0.00000 1.00000
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.099946 398 399 0.008293
After LINCS 0.000139 38 40 0.000029
Rel. Constraint Deviation: Max between atoms RMS
Before LINCS 0.001854 2177 2179 0.000406
After LINCS 0.000041 1931 1933 0.000012
Energies (kJ/mol)
Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14
6.15876e+003 3.05153e+002 2.31106e+003 2.58535e+003 5.34014e+003
LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) Potential
-3.56273e+003 -2.38143e+002 -1.54470e+004 1.38015e+002 -2.40943e+003
Kinetic En. Total Energy Temperature Pressure (bar)
6.05840e+003 3.64897e+003 2.88176e+002 2.20280e-001
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Plan on putting my cpu to 2.4GHz + with cooler temps.
You will pass me in no time 
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