Denny Frost wrote:
I don't have any domain decomposition information like that in my log
file. That's worrisome. The only other information I could find about
PME and Ewald and this set of lines:
What version of Gromacs is this?
-Justin
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 --- -------- --------
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
System total charge: 0.000
Generated table with 4400 data points for Ewald.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ6.
Tabscale = 2000 points/nm
Generated table with 4400 data points for LJ12.
Tabscale = 2000 points/nm
Configuring nonbonded kernels...
Configuring standard C nonbonded kernels...
Testing x86_64 SSE2 support... present.
Why does it say it will do PME on one line, then ordinary Ewald later?
On Fri, Jan 28, 2011 at 12:26 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Denny Frost wrote:
I just realized that that was a very old mdp file. Here is an
mdp file from my most recent run as well as what I think are the
domain decomposition statistics.
mdp file:
title = BMIM+PF6
cpp = /lib/cpp
constraints = hbonds
integrator = md
dt = 0.002 ; ps !
nsteps = 4000000 ; total 8ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = Cut-off
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc_grps = BMI PF6 tau_t =
0.2 0.2
ref_t = 300 300
nsttcouple = 1
; Energy monitoring
energygrps = BMI PF6
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = BMI PFF
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
domain decomposition
There are: 12800 Atoms
Max number of connections per atom is 63
Total number of connections is 286400
Max number of graph edges per atom is 6
Total number of graph edges is 24800
More useful information is contained at the very top of the .log
file, after the citations. An example from one of my own runs is:
Linking all bonded interactions to atoms
There are 2772 inter charge-group exclusions,
will use an extra communication step for exclusion forces for PME
The initial number of communication pulses is: X 2 Y 1
The initial domain decomposition cell size is: X 1.05 nm Y 1.58 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) 1.054 nm
atoms separated by up to 5 constraints (-rcon) 1.054 nm
When dynamic load balancing gets turned on, these settings will
change to:
The maximum number of communication pulses is: X 2 Y 2
The minimum size for domain decomposition cells is 0.833 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.79 Y 0.53
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) 0.833 nm
atoms separated by up to 5 constraints (-rcon) 0.833 nm
Making 2D domain decomposition grid 9 x 6 x 1, home cell index 0 0 0
Also, the output under "DOMAIN DECOMPOSITION STATISTICS" (at the
bottom of the file) would be useful. Also look for any notes about
performance lost due to imbalance, waiting for PME, etc. These
provide very detailed clues about how your system was treated.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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