Hi,
At this point we will need some more information in order to try and
reproduce the behavior you are seeing. Can you provide the input file,
as well as any command-line options you are using? Thanks!
-Dan
On Mon, Feb 4, 2013 at 5:31 AM, Marko Wehle <Marko.Wehle.mpikg.mpg.de> wrote:
>
> Dear Amber Developers and Users,
> unfortunatly I've did not get any better behavior of Amber12 pmemd.cuda after minimzation steps.
> Here a list of working steps, to let you know what our protocol for installation is:
>
> ###########################################
>
> tar xvfj Amber12.tar.bz2
> tar xvfj AmberTools12.tar.bz2
>
> cd $AMBERHOME
> ./patch_amber.py --update-tree
> ./patch_amber.py --update-tree
> ./patch_amber.py --update-tree
>
> # ./patch_amber.py --patch-level
>> Latest patch applied to AmberTools12: 33
>> Latest patch applied to Amber12: 14
>
> cd $AMBERHOME
> ./configure gnu
> make -j 10 install
>
> #############################################
>
> Like described in the AMBER Bugfix section of the AMBER website, we have to run the patch script several times.
> Sincerely yours,
> Marko
>
>
> -----Ursprüngliche Nachricht-----
> Von: Marko Wehle
> Gesendet: Mi 30.01.2013 21:14
> An: amber.ambermd.org
> Betreff: Re: AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
>>
>> Hello Amber Developers and Users,
>> I'm experiencing a behavior of the AMBER11 pmemd and pmemd.cuda version,
>> as well in AMBER12 pmemd.cuda, that is new to me.
>> They write out an empty restart file after minimization and put the actual
>> coordinates in an fort.16 called file.
>> Simulations do fine.
>> After a search on the web I found the following entry:
>>
>> http://archive.ambermd.org/201207/0216.html
>>
>> that exactly describes this behavior.
>> The suggestion for solving the problem was recompiling AMBER11 with all
>> patches applied.
>> Unfortunately I could not find any further comments regarding this issue.
>>
>
> bugfix.23 for Amber 11 and bugfix.7 for Amber 12 should fix this issue...
> You can use ./patch_amber.py --patch-level in Amber 12 to see which
> patches have been applied.
>
>
>> But what is irritating here, we've got this particular problem only after
>> we applied all the patches while recompiling AMBER11 and AMBER12 last week.
>> It concerns the pmemd.cuda in AMBER12 only, but in AMBER11 both pmemd and
>> pmemd.cuda.
>> Before recompiling I did not observe this issues. The compile routine and
>> the installation routine went fine so far and no errors were reported.
>>
>
> bugfix.1 for Amber 12 and bugfix.22 for Amber 11 actually introduced this
> issue, but I haven't seen them occur since the previous patches I mentioned
> were released.
>
> A temporary workaround is, of course, to use the fort.16 file instead (but
> that won't work particularly well in an automated workflow).
>
> Good luck,
> Jason
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Feb 04 2013 - 08:00:02 PST
