Log file opened: nodeid 0, nnodes = 1, host = unknown, process = 2644
G R O M A C S (-:
Groningen Machine for Chemical Simulation
VERSION 3.1.4 (-:
Copyright (c) 1991-2002, University of Groningen, The Netherlands
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_gpu (-:
++++++++ 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 = 25000001
ns_type = Simple
nstlist = 25000001
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = -10
nstlog = 125000
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 125000
nstxtcout = 125000
init_t = 150000
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 = no
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 = 4.5
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 4.5
vdwtype = Cut-off
rvdw_switch = 1.8
rvdw = 4.5
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 = Shake
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
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
solvent-model = SFSA
sasa = None
nstsasa = 1
rsasa = 0.55
epsilon_dd = 20
nstsasaout = 0
grpopts:
nrdf: 3128
ref_t: 350
tau_t: 0.1
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= 1256, targetcg= 628, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 1257
nsb->natoms: 1258
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 1258 1257 1257
---------------------------------------------------
GPU MD library 0.9 for Gromacs 3.1.4
Author: V. Vishal, Pande Group, Stanford University
NB force kernels developed in collaboration with:
Erich Elsen , Darve Group , Stanford University
Mike Houston, Graphics Group, Stanford University
Copyright(C) Pande Group, Stanford University, 2006
---------------------------------------------------
Using runtime dx9
natoms:1258
atoms: 40x32
Max number of bonds per atom is 4
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 4.5 Coulomb: 4.5 LJ: 4.5
Generated table with 500 data points for COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for LJ12.
Tabscale = 500 points/nm
Going to determine what solvent types we have.
There are 1 molecules, 1257 charge groups and 1258 atoms
There are 0 optimized solvent molecules on node 0
There are 0 optimized water molecules on node 0
GPU Warning: Output energies are not correct
Center of mass motion removal mode is Angular
We have the following groups for center of mass motion removal:
0: rest, initial mass: 8784.12
There are: 1258 Atom
Started mdrun on node 0 Mon Oct 16 15:38:32 2006
Initial temperature: 356.353 K
Downloaded coordinates to GPU
Downloaded velocities to GPU
Downloaded inverse masses to GPU
Using Shen & Freed dielectric/LJ
Initialized NB parameters
force :40x64
excl :320x640
jstrm :20x16
Initialized NB 1-4 parameters
Pair streams: 52x64
1-4 kernel uses 2x2 inverse maps
Downloaded nonbonded force paramters to GPU
Initialized GPU test
GPU initial test passed
Bondeds use 3 inverse maps for i
Bondeds use 5 inverse maps for j
Bondeds use 5 inverse maps for k
Bondeds use 2 inverse maps for l
Step Time Lambda Annealing
0 150000.01563 0.00000 1.00000
There are 1258 atoms in your xtc output selection
Initialized shakeH streams of size 25x16
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen
Numerical Integration of the Cartesian Equations of Motion of a System with
Constraints; Molecular Dynamics of n-Alkanes
J. Comp. Phys. 23 (1977) pp. 327-341
-------- -------- --- Thank You --- -------- --------
Building permutation for shuffle...done
