Hello.
Before modifying my files, I decided to see if I could run the test
simulations located at
$AMBERHOME/test/cuda/nmropt/pme/jar_distance_COM/ . I ran the command
" ./Run.jar_pbc " and the simulation failed. The error message in the
mdout file was:
CUDA (GPU): Implementation does not currently support the use of
Jarzynski simulations.
Require jar == 0 (default).
Input errors occurred. Terminating execution.
The example from $AMBERHOME/test/cuda/nmropt/pme/distance_COM/ also
fails. The error message is:
CUDA (GPU): Implementation does not currently support the use of COM
simulations.
Require iat(2) >= 0
I have already updated amber12 and ./patch_amber.py says that there
are no updates to apply. Am I doing something wrong?
Thank you
Fabricio
2012/9/18 Jason Swails <jason.swails.gmail.com>:
> On Tue, Sep 18, 2012 at 10:25 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
>
>> Hello. Thank you for the reply. It really was kind of stupid to me to
>> leave the double-quote open. As for the / character missing, there is
>> no second line in my file. The email server must have formatted the
>> text, and the result was a second line. But anyway, thank you for the
>> tip.
>> I have corrected the input and the dist.RST file now looks like this
>>
>> # Distance restraint for chain A and B (center of mass)
>> &rst restraint="distance (com(1-33.N,CA,C),com(34-66.N,CA,C))", r1=0.,
>> r2=11., r3=11., r4=35.0, rk2 = 30., rk3 = 30.,
>>
>> When I type the pmemd command, a warning appears on screen stating that:
>>
>> At line 990 of file nmr_calls.F90 (unit = 33, file = 'dist.RST')
>> Fortran runtime error: Cannot match namelist object name restraint
>>
>> I have simply copied and modified a bit the lines on the amber12
>> manual that state:
>>
>> The following are all examples of valid restraint definitions:
>> restraint = "distance( (45) (49) )"
>> = "angle (:21.C5’ :21.C4’ 108)"
>> = "torsion[-1,-1,-1, com(67, 68, 69)]"
>> = "angle( -1, plane(81, 85, 87, 90) )"
>> = "angle(plane(com(9,10),:5.CA,31,32),plane(14,15,15,16))"
>> = "coordinate(distance(:5.C3’,:6.O5’),-1.0,distance(134,-1),1.0)"
>>
>
> This syntax is specific to sander. Look at page 202 of the Amber 12 manual
> where it describes the "restraint" variable in the &rst namelist. In that
> description it says:
>
> New as of Amber 10 (sander only), users may now use a "natural language"
> system to define restraints by using the RESTRAINT character variable.
>
> If you want to use pmemd.cuda and/or pmemd with NMR restraints, you will
> need to use the "iat" variable (and "igr1" and "igr2" variables for COM
> distances). In light of this, I actually never use the "natural language"
> input myself.
>
> Note that pmemd supports only a relatively small subset of the Amber nmropt
> functionality, and pmemd.cuda supports an even more limited set. As a
> result, if you think you have an input file that should work for pmemd but
> doesn't, try it on sander. If it works, then most likely you've hit a
> pmemd limitation.
>
> HTH,
> Jason
>
> P.S. As another note -- check out the $AMBERHOME/test/nmropt/ test cases
> (only present after you've applied all Amber12 bug fixes). The Makefile
> lists all of the tests that work with pmemd (and you can find the
> pmemd.cuda-compatible ones in $AMBERHOME/test/cuda/nmropt). My suggestion
> is to adapt one of these input files to your system (since these are known
> to work for pmemd and pmemd.cuda, respectively).
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> AMBER.ambermd.org
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Received on Tue Sep 18 2012 - 22:30:02 PDT
