AMBER Archive (2004)

Subject: Re: AMBER: Minimization error

From: opitz_at_che.udel.edu
Date: Tue Aug 24 2004 - 16:09:15 CDT

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Dear Dr. Walker and Amber Community,

I am running a minimization on an Octane and a Cluster. On my Octane
there were several warnings of this nature "RESTARTED DUE TO LINMIN
FAILURE", while there weren't on the cluster.
Following Dr. Walkers suggestion I ran this on both machines with
different numbers of processors. Again, the linmin failure only happens
on the Octane system.
When comparing the energies at the end of each run, there are similar
energies for the same number of processors. Also, when comparing the
structures in Moil-view they look very similar.

The tests that Dr. Walker asked about, they passed on Octane with just a
few warnings, but they turned out to be rounding errors. On the cluster I
am not certain, as the system administrator had installed Amber7 there.

I have appended the final results output from each of the runs as well as
attached an excel spreadsheet with these results a bit more organized. My
question is, which of these states is acceptable? Are all of these wrong?
What should my next step be? Can I take one of these structures over
another and run MD on them? Some suggestions of how to deal with this
would be very welcome.

Best Regards,

Armin

Cluster, 1 processor
 NSTEP ENERGY RMS GMAX NAME NUMBER
  10000 -3.5386E+02 4.2995E-01 2.1918E+00 H4 970

 BOND = 28.7085 ANGLE = 276.2950 DIHED = 342.8602
 VDWAALS = -194.5266 EEL = 0.6367 HBOND = 0.0000
 1-4 VDW = 170.6297 1-4 EEL = -978.4673 RESTRAINT = 0.0000

Cluster, 2 processors
 NSTEP ENERGY RMS GMAX NAME NUMBER
  10000 -5.6080E+02 1.9868E-01 8.0435E-01 H11 382

 BOND = 27.6700 ANGLE = 219.6259 DIHED = 310.2828
 VDWAALS = -233.0950 EEL = -63.1986 HBOND = 0.0000
 1-4 VDW = 156.4703 1-4 EEL = -978.5568 RESTRAINT = 0.0000

Cluster, 4 processors
 NSTEP ENERGY RMS GMAX NAME NUMBER
  10000 -1.9055E+02 7.2962E-01 3.7201E+00 H8 470

 BOND = 32.7074 ANGLE = 315.9480 DIHED = 350.8248
 VDWAALS = -113.1678 EEL = 1.1835 HBOND = 0.0000
 1-4 VDW = 198.3012 1-4 EEL = -976.3509 RESTRAINT = 0.0000

Octane, 1 processor
 NSTEP ENERGY RMS GMAX NAME NUMBER
   9223 -4.6784E+02 3.1572E-01 2.9213E+00 N1 574

 BOND = 27.5847 ANGLE = 254.6660 DIHED = 324.6847
 VDWAALS = -212.0963 EEL = -49.0792 HBOND = 0.0000
 1-4 VDW = 164.6040 1-4 EEL = -978.2072 RESTRAINT = 0.0000

     ***** REPEATED LINMIN FAILURE *****

Octane, 2 processors
 NSTEP ENERGY RMS GMAX NAME NUMBER
   8567 -5.4532E+02 2.3128E-01 9.4289E-01 H7 450

 BOND = 27.6072 ANGLE = 233.3834 DIHED = 316.5635
 VDWAALS = -229.5771 EEL = -72.2528 HBOND = 0.0000
 1-4 VDW = 158.3414 1-4 EEL = -979.3807 RESTRAINT = 0.0000

     ***** REPEATED LINMIN FAILURE *****

==============Original message text===============
On Fri, 20 Aug 2004 18:48:27 EDT "Ross Walker" wrote:

Dear Armin,

The restarted due to linmin failure often happens when the minimiser stops
going anywhere during a minimisation. This can occur if you have minimised a
long way and have reached a minimum. It can also occur if you try to
minimise your system too far with shake turned on. The minimiser wants to
move the hydrogen bonds but can't because of shake.

It is strange, however, that you only see this on one machine. You are
certain the runs are identical on the two machines? How about if you just
run it on 2 processors on the cluster? I suspect that there may be a problem
somewhere. Try running single cpu on the octane and see what you get.

BTW, do all of the tests on the machines pass? Both with single cpu, 2 cpu
and 4 cpu? If they don't then there is definitely a problem with your
installation.

Get back to me with the results of the tests.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |


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