On Thu, 14 Sep 2006, David van der Spoel wrote:
Atte Sillanpää wrote:
On Thu, 14 Sep 2006, David van der Spoel wrote:
I've run into a mysterious problem. The versions 3.3. and 3.3.1 compile
and execute, but the short range coulomb and LJ energies come out as zero
when using the mpi-version. Serial code works ok (mpi version gives zero
if run using just one cpu). No errors, no warnings.
...
if you suspect PME, then try running without it.
Hi again,
the short range energies come out as zero with all electrostatic methods
cut-off, PME, shift. But only the short range. Other components get some
numbers (and you _can_ continue the simulation for at least thousands of
steps).
can you try a small water box on one processor?
just to eliminate problems. if you can simulate, that means the forces are
correct (or zero too...) try printing the forces in other words.
just do one step with all output turned on.
Hi,
tried that. Forces are almost zero in a small water system (4 first
molecules of spc216.gro) as calculated with mdrun_mpi using one
processor. With the serial version I get bigger values.
I then enlarged the box and increased electrostatics and vdw cutoffs
(no PME) to 3 nm so that all atoms feel short range interactions. Now
if I compare the forces they are identical for the first 13 atoms (and
the x-component for the 14th) and then they differ as shown below.
Here are the outputs from veloc.xvg (g_traj -ov ) for the mdrun_mpi
(one step, no initial velocities):
0.000000000 -0.000000596 -0.000000834
0.000000000 0.000014305 -0.000000834
0.000000000 0.000014305 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 0.000001267 -0.000000834
0.000000000 -0.000008047 -0.000000834
0.000000000 -0.000009909 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 0.000058771
0.000000000 -0.000000596 -0.000000834
0.001000000 -0.000002319 0.000021988
0.000000730 -0.000017221 0.000021988
0.000000730 -0.000002319 0.000021988
0.000008180 0.000042384 -0.000037617
0.000000730 -0.000121529 -0.000067419
0.000000730 0.000057285 -0.000007814
0.000000730 -0.000002319 0.000021988
0.000000730 0.000474518 -0.000007814
-0.000058875 -0.000002319 0.000021988
0.000000730 -0.000061924 0.000021988
0.000000730 -0.000121529 0.000021988
0.000000730 0.000116890 -0.000454849
and for mdrun, serial version:
0.000000000 -0.000000596 -0.000000834
0.000000000 0.000014305 -0.000000834
0.000000000 0.000014305 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 0.000001267 -0.000000834
0.000000000 -0.000008047 -0.000000834
0.000000000 -0.000009909 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 0.000058771
0.000000000 -0.000000596 -0.000000834
0.001000000 0.000445691 0.000485396
-0.000728320 0.003858060 -0.001481560
0.007869650 -0.007034690 -0.000647092
-0.000296186 0.000058261 -0.000170255
-0.000072669 -0.001506360 0.001558280
0.000881006 -0.001148730 0.002094720
0.000404169 -0.000046048 0.000485396
-0.000668715 0.000430790 -0.003686930
0.005530170 -0.001476560 -0.006100920
0.007437520 -0.000165257 -0.000408674
0.000404169 0.000609603 0.001498670
-0.002456850 0.001622880 0.000545001
The difference being:
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000000000 0.000000000
0.000000000 0.000448010 0.000463408
-0.000729050 0.003875281 -0.001503548
0.007868920 -0.007032371 -0.000669080
-0.000304366 0.000015876 -0.000132638
-0.000073398 -0.001384831 0.001625699
0.000880276 -0.001206015 0.002102534
0.000403439 -0.000043728 0.000463408
-0.000669445 -0.000043728 -0.003679116
0.005589045 -0.001474241 -0.006122908
0.007436790 -0.000103333 -0.000430662
0.000403439 0.000731132 0.001476682
-0.002457580 0.001505990 0.000999850
Something starts to go wrong after the first few atoms? Also if I
reduce the cutoffs to 0.1 nm, I get short range nonbondeds as zero in
both serial and parallel and also other energies identical.
These are the forces without any short range forces (cutoff 0.1 nm):
0.000000000 -0.000000596 -0.000000834
0.000000000 0.000014305 -0.000000834
0.000000000 0.000014305 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 0.000001267 -0.000000834
0.000000000 -0.000008047 -0.000000834
0.000000000 -0.000009909 -0.000000834
0.000000000 -0.000000596 -0.000000834
0.000000000 -0.000000596 0.000058771
0.000000000 -0.000000596 -0.000000834
0.001000000 -0.000002319 0.000021988
0.000000730 -0.000017221 0.000021988
0.000000730 -0.000002319 0.000021988
0.000008180 0.000042384 -0.000037617
0.000000730 -0.000121529 -0.000067419
0.000000730 0.000057285 -0.000007814
0.000000730 -0.000002319 0.000021988
0.000000730 0.000474518 -0.000007814
-0.000058875 -0.000002319 0.000021988
0.000000730 -0.000061924 0.000021988
0.000000730 -0.000121529 0.000021988
0.000000730 0.000116890 -0.000454849
Cheers,
Atte
Cheers,
Atte
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
_______________________________________________
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