Is tpbconv with the "pbc" option the best way to make the molecules whole again?<br><br><div class="gmail_quote">On Wed, Feb 9, 2011 at 2:06 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 class="im"><br>
<br>
Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This run is actually a combination of two 5x5x5 nm boxes, one if which was previously run in DD, and the other is water. Since the length of that bond is almost 5 nm, is it possible that the pbc's are not being recognized? There is no way I have a bond that long from my previous run.<br>
<br>
</blockquote>
<br></div>
I'll venture a guess that there were broken molecules in the system you concatenated? That would gel with a bond that stretches across a 5-nm box. You have to deal with whole molecules in the input configuration.<br>
<br>
-Justin<br>
<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">
On Wed, Feb 9, 2011 at 1:56 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Denny Frost wrote:<br>
<br>
I'm using version 4.5.3<br>
<br>
Here's the output from the log file from DD initiation to the error:<br>
<br>
Initializing Domain Decomposition on 8 nodes<br>
Dynamic load balancing: auto<br>
Will sort the charge groups at every domain (re)decomposition<br>
Initial maximum inter charge-group distances:<br>
two-body bonded interactions: 4.893 nm, Bond, atoms 8994 8996<br>
multi-body bonded interactions: 4.893 nm, Angle, atoms 8994 8997<br>
Minimum cell size due to bonded interactions: 5.382 nm<br>
<br>
<br>
Bonded interactions should normally not occur over such a length.<br>
The information printed here points to the culprits. What are<br>
these atoms, and why are they bonded if they are so far away?<br>
<br>
-Justin<br>
<br>
Using 0 separate PME nodes<br>
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25<br>
Optimizing the DD grid for 8 cells with a minimum initial size<br>
of 6.728 nm<br>
The maximum allowed number of cells is: X 0 Y 0 Z 1<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi, VERSION 4.5.3<br>
Source code file: domdec.c, line: 6428<br>
<br>
Fatal error:<br>
There is no domain decomposition for 8 nodes that is compatible<br>
with the given box and a minimum cell size of 6.72787 nm<br>
Change the number of nodes or mdrun option -rdd or -dds<br>
Look in the log file for details on the domain decomposition<br>
For more information and tips for troubleshooting, please check<br>
the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
<br>
And here is my mdp file<br>
<br>
title = BMIM+PF6<br>
cpp = /lib/cpp<br>
constraints = hbonds<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 75000 ; total 150 ps<br>
nstcomm = 10<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 SOL tau_t = 0.2 0.2 0.2<br>
ref_t = 300 300 300<br>
nsttcouple = 1<br>
; Energy monitoring<br>
energygrps = BMI PF6 SOL<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>
pcoupltype = isotropic<br>
;pc-grps = BMI PFF<br>
tau_p = 2.0<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>
<br>
On Wed, Feb 9, 2011 at 1:39 PM, Justin A. Lemkul<br>
<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br></div></div><div><div></div><div class="h5">
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>> wrote:<br>
<br>
<br>
<br>
Denny Frost wrote:<br>
<br>
I am trying to start a run using domain decomposition on a<br>
5x5x10 nm box with about 26,000 atoms in it. I've tried<br>
running<br>
8-16 pp nodes, but gromacs always throws an error saying that<br>
there is no domain decomposition compatible with this box<br>
and a<br>
minimum cell size of 6.728 nm. I've tried many values<br>
for -dds<br>
and a few dd vectors, but with no luck. Does anyone know<br>
to get<br>
domain decomposition working on a rectangular system like<br>
this?<br>
<br>
<br>
Not without significantly more information. Please post:<br>
<br>
1. Your Gromacs version<br>
2. Any DD-related information that is printed to either the<br>
log file<br>
or stdout<br>
3. Your .mdp file<br>
<br>
-Justin<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></div></div>
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<br>
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<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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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>
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-- <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>
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