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
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Received on Mon Feb 04 2013 - 05:00:03 PST
