gromacs 4.5.1<br><br><div class="gmail_quote">On Fri, Jan 28, 2011 at 12:40 PM, Erik Marklund <span dir="ltr"><<a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">
PME is still an Ewald sum.<br>
<br>
Erik<br>
<br>
Denny Frost skrev 2011-01-28 20.38:
<div><div></div><div class="h5"><blockquote type="cite">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" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
<div>
<div><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);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><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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</blockquote>
</div>
<br>
</div>
</blockquote>
<br>
<br>
</div></div><pre cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a href="mailto:erikm@xray.bmc.uu.se" target="_blank">erikm@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se/</a>
</pre>
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