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:<div><br></div><div><div>Table routines are used for coulomb: TRUE</div>
<div>Table routines are used for vdw: FALSE</div><div>Will do PME sum in reciprocal space.</div><div><br></div><div>++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++</div><div>U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen </div>
<div>A smooth particle mesh Ewald method</div><div>J. Chem. Phys. 103 (1995) pp. 8577-8592</div><div>-------- -------- --- Thank You --- -------- --------</div><div><br></div><div>Will do ordinary reciprocal space Ewald sum.</div>
<div>Using a Gaussian width (1/beta) of 0.384195 nm for Ewald</div><div>Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2</div><div>System total charge: 0.000</div><div>Generated table with 4400 data points for Ewald.</div>
<div>Tabscale = 2000 points/nm</div><div>Generated table with 4400 data points for LJ6.</div><div>Tabscale = 2000 points/nm</div><div>Generated table with 4400 data points for LJ12.</div><div>Tabscale = 2000 points/nm</div>
<div>Configuring nonbonded kernels...</div><div>Configuring standard C nonbonded kernels...</div><div>Testing x86_64 SSE2 support... present.</div><div><br></div><div><br></div><div>Why does it say it will do PME on one line, then ordinary Ewald later?</div>
<br><div class="gmail_quote">On Fri, Jan 28, 2011 at 12:26 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.<br>
<br>
mdp file:<br>
title = BMIM+PF6<br>
cpp = /lib/cpp<br>
constraints = hbonds<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 4000000 ; total 8ns.<br>
nstcomm = 1<br>
nstxout = 50000<br>
nstvout = 50000<br>
nstfout = 0<br>
nstlog = 5000<br>
nstenergy = 5000<br>
nstxtcout = 25000<br>
nstlist = 10<br>
ns_type = grid<br>
pbc = xyz<br>
coulombtype = PME<br>
vdwtype = Cut-off<br>
rlist = 1.2<br>
rcoulomb = 1.2<br>
rvdw = 1.2<br>
fourierspacing = 0.12<br>
pme_order = 4<br>
ewald_rtol = 1e-5<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc_grps = BMI PF6 tau_t = 0.2 0.2<br>
ref_t = 300 300<br>
nsttcouple = 1<br>
; Energy monitoring<br>
energygrps = BMI PF6<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>
pcoupltype = isotropic<br>
;pc-grps = BMI PFF<br>
tau_p = 1.0<br>
ref_p = 1.0<br>
compressibility = 4.5e-5<br>
<br>
; Generate velocites is off at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 100000<br>
<br>
domain decomposition<br>
There are: 12800 Atoms<br>
Max number of connections per atom is 63<br>
Total number of connections is 286400<br>
Max number of graph edges per atom is 6<br>
Total number of graph edges is 24800<br>
<br>
</blockquote>
<br></div></div>
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:<br>
<br>
Linking all bonded interactions to atoms<br>
There are 2772 inter charge-group exclusions,<br>
will use an extra communication step for exclusion forces for PME<br>
<br>
The initial number of communication pulses is: X 2 Y 1<br>
The initial domain decomposition cell size is: X 1.05 nm Y 1.58 nm<br>
<br>
The maximum allowed distance for charge groups involved in interactions is:<br>
non-bonded interactions 1.400 nm<br>
(the following are initial values, they could change due to box deformation)<br>
two-body bonded interactions (-rdd) 1.400 nm<br>
multi-body bonded interactions (-rdd) 1.054 nm<br>
atoms separated by up to 5 constraints (-rcon) 1.054 nm<br>
<br>
When dynamic load balancing gets turned on, these settings will change to:<br>
The maximum number of communication pulses is: X 2 Y 2<br>
The minimum size for domain decomposition cells is 0.833 nm<br>
The requested allowed shrink of DD cells (option -dds) is: 0.80<br>
The allowed shrink of domain decomposition cells is: X 0.79 Y 0.53<br>
The maximum allowed distance for charge groups involved in interactions is:<br>
non-bonded interactions 1.400 nm<br>
two-body bonded interactions (-rdd) 1.400 nm<br>
multi-body bonded interactions (-rdd) 0.833 nm<br>
atoms separated by up to 5 constraints (-rcon) 0.833 nm<br>
<br>
<br>
Making 2D domain decomposition grid 9 x 6 x 1, home cell index 0 0 0<br>
<br>
<br>
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.<br>
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</div></div></blockquote></div><br></div>