> That was a long mail. How about T-coupling? Which algorithm did you use?
Sorry for the long mail. For T-coupling I used Berendsen al gorithm.
> Did you do a diff on the md.log to check for differences in the mdp
> parameters?
Yes, I attach the diff file (emended of references and other comments), as
well as the run parameters reported in the NEW md log file.
For system 1 I tried both the same tpr file (from 3.3.1) in 3.3.1 and
4.0.4 simulations, and a new 4.0.4 format tpr file with grompp for 4.0.4
md run, but all simulations stopped in about 2,000 steps.
System 2, for which I attached the different parts of the log files, was
simulated using the same tpr file (from 3.3.1) for both 3.3.1 and 4.0.4 MD
runs.
> Did you run these in parallel? What happens when you run it
> sequentially? And what happens in single precision?
For system 1, changing precision, compiler or serial-vs-parallel run only
affect the exact step at which the simulation stops. Also for system 2
these parameters do not affect the overall oscillating behaviour of the
simulation.
Best,
Pietro
--
Dr. Pietro Amodeo, PhD.
Istituto di Chimica Biomolecolare del CNR
Comprensorio "A. Olivetti", Edificio 70
Via Campi Flegrei 34
I-80078 Pozzuoli (Napoli) - Italy
Phone +39-0818675072
Fax +39-0818041770
Email [email protected]
11c11
< :-) VERSION 3.3.1 (-:
---
> :-) VERSION 4.0.4 (-:
40,65d55
< CPU= 0, lastcg= 1461, targetcg= 6589, myshift= 5
< CPU= 1, lastcg= 2717, targetcg= 7845, myshift= 5
< CPU= 2, lastcg= 3973, targetcg= 9101, myshift= 5
< CPU= 3, lastcg= 5229, targetcg= 102, myshift= 5
< CPU= 4, lastcg= 6485, targetcg= 1358, myshift= 4
< CPU= 5, lastcg= 7740, targetcg= 2612, myshift= 4
< CPU= 6, lastcg= 8998, targetcg= 3870, myshift= 4
< CPU= 7, lastcg=10255, targetcg= 5128, myshift= 4
< nsb->shift = 5, nsb->bshift= 0
< Listing Scalars
< nsb->nodeid: 0
< nsb->nnodes: 8
< nsb->cgtotal: 10256
< nsb->natoms: 30126
< nsb->shift: 5
< nsb->bshift: 0
< Nodeid index homenr cgload workload
< 0 0 3766 1462 1462
< 1 3766 3766 2718 2718
< 2 7532 3766 3974 3974
< 3 11298 3766 5230 5230
< 4 15064 3766 6486 6486
< 5 18830 3765 7741 7741
< 6 22595 3766 8999 8999
< 7 26361 3765 10256 10256
<
73,74d62
< bDomDecomp = FALSE
< decomp_dir = 0
77d64
< nstcheckpoint = 1000
96c83,84
< bUncStart = FALSE
---
> bPeriodicMols = FALSE
> bContinuation = FALSE
109a98,106
> 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
111a109
> rtpi = 0.05
120a119
> implicit_solvent = No
121a121
> gb_epsilon_solvent = 80
125c125,128
< implicit_solvent = No
---
> gb_obc_alpha = 1
> gb_obc_beta = 0.8
> gb_obc_gamma = 4.85
> sa_surface_tension = 2.092
127d129
< fudgeQQ = 1
133a136,144
> 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
143,144d153
< dihre-tau = 0
< nstdihreout = 100
152c161
< shake_tol = 1e-04
---
> shake_tol = 0.0001
199,216d207
< Max number of graph edges per atom is 4
< Table routines are used for coulomb: TRUE
< Table routines are used for vdw: FALSE
< Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
< Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4
< System total charge: 0.000
< Generated table with 1200 data points for Ewald.
< Tabscale = 500 points/nm
< Generated table with 1200 data points for LJ6.
< Tabscale = 500 points/nm
< Generated table with 1200 data points for LJ12.
< Tabscale = 500 points/nm
< Generated table with 500 data points for 1-4 COUL.
< Tabscale = 500 points/nm
< Generated table with 500 data points for 1-4 LJ6.
< Tabscale = 500 points/nm
< Generated table with 500 data points for 1-4 LJ12.
< Tabscale = 500 points/nm
218c209,224
< Enabling SPC water optimization for 9451 molecules.
---
> Initializing Domain Decomposition on 8 nodes
> Dynamic load balancing: auto
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
> two-body bonded interactions: 0.614 nm, LJ-14, atoms 1485 1492
> multi-body bonded interactions: 0.614 nm, Proper Dih., atoms 1485 1492
> Minimum cell size due to bonded interactions: 0.675 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
> Estimated maximum distance required for P-LINCS: 0.876 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Using 0 separate PME nodes
> Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
> Optimizing the DD grid for 8 cells with a minimum initial size of 1.095 nm
> The maximum allowed number of cells is: X 5 Y 5 Z 5
> Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
> Domain decomposition nodeid 0, coordinates 0 0 0
219a226,227
> Table routines are used for coulomb: TRUE
> Table routines are used for vdw: FALSE
228,231c236,257
< Parallelized PME sum used.
< PARALLEL FFT DATA:
< local_nx: 8 local_x_start: 0
< local_ny_after_transpose: 8 local_y_start_after_transpose 0
---
> Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
> Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4
> System total charge: 0.000
> Generated table with 4799 data points for Ewald.
> Tabscale = 2000 points/nm
> Generated table with 4799 data points for LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4799 data points for LJ12.
> Tabscale = 2000 points/nm
> Generated table with 4799 data points for 1-4 COUL.
> Tabscale = 2000 points/nm
> Generated table with 4799 data points for 1-4 LJ6.
> Tabscale = 2000 points/nm
> Generated table with 4799 data points for 1-4 LJ12.
> Tabscale = 2000 points/nm
>
> Enabling SPC water optimization for 9451 molecules.
>
> Configuring nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
>
233,237d258
< Done rmpbc
< Center of mass motion removal mode is Linear
< We have the following groups for center of mass motion removal:
< 0: rest, initial mass: 189902
< There are: 3766 Atoms
239c260
< Constraining the starting coordinates (step -2)
---
> Initializing Parallel LINear Constraint Solver
246a268,270
> The number of constraints is 1787
> There are inter charge-group constraints,
> will communicate selected coordinates each lincs iteration
255a280,311
> Linking all bonded interactions to atoms
> There are 6229 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: X 1 Y 1
> The initial domain decomposition cell size is: X 1.55 nm Y 3.02 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.400 nm
> (the following are initial values, they could change due to box deformation)
> two-body bonded interactions (-rdd) 1.400 nm
> multi-body bonded interactions (-rdd) 1.400 nm
> atoms separated by up to 5 constraints (-rcon) 1.551 nm
>
> When dynamic load balancing gets turned on, these settings will change to:
> The maximum number of communication pulses is: X 2 Y 1
> The minimum size for domain decomposition cells is 1.082 nm
> The requested allowed shrink of DD cells (option -dds) is: 0.80
> The allowed shrink of domain decomposition cells is: X 0.70 Y 0.46
> The maximum allowed distance for charge groups involved in interactions is:
> non-bonded interactions 1.400 nm
> two-body bonded interactions (-rdd) 1.400 nm
> multi-body bonded interactions (-rdd) 1.082 nm
> atoms separated by up to 5 constraints (-rcon) 1.082 nm
>
>
> Making 2D domain decomposition grid 4 x 2 x 1, home cell index 0 0 0
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
>
261a318,320
> There are: 30126 Atoms
> Charge group distribution at step 0: 1295 1280 1281 1276 1309 1258 1283 1274
> Grid: 11 x 13 x 9 cells
263,278c322
< Initializing LINear Constraint Solver
< number of constraints is 1787
< average number of constraints coupled to one constraint is 2.9
<
< Rel. Constraint Deviation: Max between atoms RMS
< Before LINCS 0.032909 340 341 0.006025
< After LINCS 0.000481 509 511 0.000072
<
< Going to use C-settle (668 waters)
< wo = 0.888096, wh =0.0559521, wohh = 18.0154, rc = 0.08165, ra = 0.00646074
< rb = 0.0512738, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
<
< Constraining the coordinates at t0-dt (step -1)
< Rel. Constraint Deviation: Max between atoms RMS
< Before LINCS 0.102061 310 311 0.017326
< After LINCS 0.000231 858 860 0.000037
---
> Constraining the starting coordinates (step 0)
280c324,325
< Started mdrun on node 0 Thu Nov 20 16:46:22 2008
---
> Constraining the coordinates at t0-dt (step 0)
> RMS relative constraint deviation after constraining: 3.73e-05
281a327
>
Log file opened on Thu Mar 12 15:53:42 2009
Host: e4hpc01 pid: 23358 nodeid: 0 nnodes: 8
The Gromacs distribution was built Thu Mar 12 14:40:48 CET 2009 by
r...@e4hpc01 (Linux 2.6.18-53.el5 x86_64)
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 4.0.4 (-:
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.
:-) /root/NFS/Gromacs/bin/mdrun_mpi_d (double precision) (-:
++++ 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 --- -------- --------
parameters of the run:
integrator = md
nsteps = 50000
init_step = 0
ns_type = Grid
nstlist = 10
ndelta = 2
nstcomm = 1
comm_mode = Linear
nstlog = 10
nstxout = 250
nstvout = 1000
nstfout = 0
nstenergy = 10
nstxtcout = 0
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 64
nky = 64
nkz = 63
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = Parrinello-Rahman
epctype = Isotropic
tau_p = 0.5
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
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
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
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
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
delta_lambda = 0
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 = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
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_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: 3489.83 56703.2 41.9979
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
energygrp_flags[ 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
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 0.614 nm, LJ-14, atoms 1485 1492
multi-body bonded interactions: 0.614 nm, Proper Dih., atoms 1485 1492
Minimum cell size due to bonded interactions: 0.675 nm
Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.876 nm
Estimated maximum distance required for P-LINCS: 0.876 nm
This distance will limit the DD cell size, you can override this with -rcon
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 1.095 nm
The maximum allowed number of cells is: X 5 Y 5 Z 5
Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
Domain decomposition nodeid 0, coordinates 0 0 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------
Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Cut-off's: NS: 1 Coulomb: 1 LJ: 1.4
System total charge: 0.000
Generated table with 4799 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4799 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4799 data points for LJ12.
Tabscale = 2000 points/nm
Generated table with 4799 data points for 1-4 COUL.
Tabscale = 2000 points/nm
Generated table with 4799 data points for 1-4 LJ6.
Tabscale = 2000 points/nm
Generated table with 4799 data points for 1-4 LJ12.
Tabscale = 2000 points/nm
Enabling SPC water optimization for 9451 molecules.
Configuring nonbonded kernels...
Testing x86_64 SSE2 support... present.
Removing pbc first time
Initializing Parallel LINear Constraint Solver
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess
P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 116-122
-------- -------- --- Thank You --- -------- --------
The number of constraints is 1787
There are inter charge-group constraints,
will communicate selected coordinates each lincs iteration
++++ 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 --- -------- --------
Linking all bonded interactions to atoms
There are 6229 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 1.55 nm Y 3.02 nm
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.400 nm
(the following are initial values, they could change due to box deformation)
two-body bonded interactions (-rdd) 1.400 nm
multi-body bonded interactions (-rdd) 1.400 nm
atoms separated by up to 5 constraints (-rcon) 1.551 nm
When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 2 Y 1
The minimum size for domain decomposition cells is 1.082 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.70 Y 0.46
The maximum allowed distance for charge groups involved in interactions is:
non-bonded interactions 1.400 nm
two-body bonded interactions (-rdd) 1.400 nm
multi-body bonded interactions (-rdd) 1.082 nm
atoms separated by up to 5 constraints (-rcon) 1.082 nm
Making 2D domain decomposition grid 4 x 2 x 1, home cell index 0 0 0
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: 30126 Atoms
Charge group distribution at step 0: 1295 1280 1281 1276 1309 1258 1283 1274
Grid: 11 x 13 x 9 cells
Constraining the starting coordinates (step 0)
Constraining the coordinates at t0-dt (step 0)
RMS relative constraint deviation after constraining: 3.73e-05
Initial temperature: 300.99 K
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