Hello,
On Fri, Feb 5, 2010 at 9:55 AM, Mark Dixon <m.c.dixon.leeds.ac.uk> wrote:
> Hi,
>
> I'm trying to get my build of AMBER10 (64-bit, Intel 11.1.059 + MKL) to pass
> the test suite before giving it to my users. The following failure does not
> appear in the archives and I was wondering if someone could help, please.
>
> I'm getting (with or without using MKL):
>
> possible FAILURE: check mdout.jar.dif
> /apps/applications/amber/10/1/default/test/jar
> 87c87
> < R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 =
> 5000.000
> ---
>>
>> R1 = 0. R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 =
>> 5000.000
>
> ---------------------------------------
> possible FAILURE: check mdout.jar.000.dif
> /apps/applications/amber/10/1/default/test/jar_multi
> 87c87
> < R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 =
> 5000.000
>>
>> R1 = 0. R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 =
>> 5000.000
>
> ### Maximum absolute error in matching lines = 8.50e+01 at line 87 field 3
> ### Maximum relative error in matching lines = 1.00e+00 at line 87 field 3
> ---------------------------------------
> possible FAILURE: check mdout.jar.001.dif
> /apps/applications/amber/10/1/default/test/jar_multi
> 87c87
> < R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 =
> 5000.000
>>
>> R1 = 0. R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 =
>> 5000.000
>
> ### Maximum absolute error in matching lines = 8.50e+01 at line 87 field 3
> ### Maximum relative error in matching lines = 1.00e+00 at line 87 field 3
>
>
> i.e. R1 is 0. instead of -85.000. Page 111 of the manual indicates that this
> is an internally set parameter.
>
> I asked a local AMBER user and they thought that this was bonkers - as the
> line wasn't even in the results section, and that the results section was in
> perfect agreement (jar) or within 4 d.p. (jar_multi).
This is indeed an input variable, and defines the point at which the
flat-well potential becomes linear. The fact that the results are
identical means that the simulation never visits dihedral angles less
than 0 degrees, so the potential never appears different.
It appears as though r1 has been removed from the test input file, so
it returned to its default value of 0. This is safe to ignore.
>
> It'd be great if someone can confirm I can ignore this. And does anyone know
> what is going on here?
>
> Thanks,
>
> Mark
> --
> -----------------------------------------------------------------
> Mark Dixon Email : m.c.dixon.leeds.ac.uk
> HPC/Grid Systems Support Tel (int): 35429
> Information Systems Services Tel (ext): +44(0)113 343 5429
> University of Leeds, LS2 9JT, UK
> -----------------------------------------------------------------
>
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>
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Feb 05 2010 - 07:30:02 PST
