AMBER Archive (2004)

Subject: RE: AMBER: Minimization error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 20 2004 - 17:48:27 CDT

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 |
 

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of opitz_at_che.udel.edu
> Sent: 20 August 2004 12:44
> To: amber_at_scripps.edu
> Subject: AMBER: Minimization error
>
> Dear Amber Community,
>
> I am running a minimization of a polymer on two different
> systems, same
> input parameters.
> The one system is running on an octane with 2 processors, the
> other run
> is run on a cluster where it uses 4 processors.
> The run on octane starts to show "Restarted due to Linmin
> failure" after
> some time, while the cluster does not. Why does this happen, and what
> does it mean?
>
> I will include the output right before this error from both files:
>
> Octane:
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 6150 -3.2323E+02 3.8800E-01 1.4320E+00 O1
> 954
>
> BOND = 28.8011 ANGLE = 291.2992 DIHED
> = 348.4638
> VDWAALS = -203.5855 EEL = 18.4040 HBOND
> = 0.0000
> 1-4 VDW = 170.3680 1-4 EEL = -976.9805 RESTRAINT
> = 0.0000
>
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 6200 -3.7139E+02 2.0144E+00 4.9200E+01 C3
> 464
>
> BOND = 30.3892 ANGLE = 261.0022 DIHED
> = 328.8931
> VDWAALS = -186.4758 EEL = 2.8240 HBOND
> = 0.0000
> 1-4 VDW = 170.3365 1-4 EEL = -978.3610 RESTRAINT
> = 0.0000
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 6250 -4.1619E+02 1.5099E+00 2.0467E+01 C5
> 579
>
> BOND = 30.1880 ANGLE = 261.8499 DIHED
> = 327.0155
> VDWAALS = -197.5285 EEL = -29.1312 HBOND
> = 0.0000
> 1-4 VDW = 169.8159 1-4 EEL = -978.3960 RESTRAINT
> = 0.0000
>
>
> Cluster:
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 6150 -1.9179E+02 7.3055E-01 3.7243E+00 H8
> 470
>
> BOND = 32.7233 ANGLE = 315.9918 DIHED
> = 350.8293
> VDWAALS = -113.0110 EEL = -0.3157 HBOND
> = 0.0000
> 1-4 VDW = 198.3466 1-4 EEL = -976.3527 RESTRAINT
> = 0.0000
>
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 6200 -1.9179E+02 7.3054E-01 3.7243E+00 H8
> 470
>
> BOND = 32.7231 ANGLE = 315.9913 DIHED
> = 350.8292
> VDWAALS = -113.0129 EEL = -0.3157 HBOND
> = 0.0000
> 1-4 VDW = 198.3461 1-4 EEL = -976.3527 RESTRAINT
> = 0.0000
>
>
> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 6250 -1.9179E+02 7.3053E-01 3.7242E+00 H8
> 470
>
> BOND = 32.7229 ANGLE = 315.9908 DIHED
> = 350.8291
> VDWAALS = -113.0148 EEL = -0.3157 HBOND
> = 0.0000
> 1-4 VDW = 198.3455 1-4 EEL = -976.3527 RESTRAINT
> = 0.0000
>
>
> Thanks,
>
> Armin
>
>
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