Hi Marek,
I managed to get this installed. Not sure why you got that error. Perhaps
give it another try. :)
└──21:25──$ ./update_amber -v
Version is reported as <version>.<patches applied>
AmberTools version 13.06
Amber version 12.18
#######
└──21:25──$ ./update_amber --show-applied-patches
AmberTools 13 Applied Patches:
------------------------------
update.1 (modifies cpptraj)
update.2 (modifies MMPBSA.py, and, ParmEd)
update.3 (modifies cpptraj, ParmEd, calcpka)
update.4 (modifies pbsa)
update.5 (modifies cpptraj, MMPBSA.py, ParmEd)
update.6 (modifies configure2)
Amber 12 Applied Patches:
-------------------------
bugfix.1, bugfix.2, bugfix.3, bugfix.4, bugfix.5, bugfix.6, bugfix.7,
bugfix.8, bugfix.9, bugfix.10,
bugfix.11, bugfix.12, bugfix.13, bugfix.14, bugfix.15, bugfix.16,
bugfix.17, bugfix.18
br,
g
On 1 June 2013 19:22, Marek Maly <marek.maly.ujep.cz> wrote:
> Dear all,
> I just found that in Updates section ( http://ambermd.org/bugfixes12.html
> ) is already record of the
> expected bugfix-18 announced recently by Ross.
>
> i.e.
> --------
> bugfix.18: Fixes a number of issues with pmemd and pmemd.cuda:
> Updates GPU code to v12.3
> Adds check to prevent running ntb=2 with gamma_ln=0 and ntt=3 or 4.
> Fixes Hamiltonian Replica Exchange on GPUs and CPUs in explicit solvent.
> Fixes issue with nmropt DUMPAVE printing in pmemd for H-REMD.
> Fixes extra-points support for the GLYCAM force field which was leading to
> a segfault in pmemd and pmemd.cuda.
> Improves stability for NPT simulations on GPUs.
> Adds check to make sure code quits if skinnb would go negative in GPU
> calculations due to large reductions in box size.
> Fixes issues with restart of NPT simulations on GPUs in cases where the
> box size had shrunk considerably.
> Fixes minimizations on GPUs with the SPFP precision model by truncating
> large forces that occur during the beginning of a minimization.
> Changes pmemd.cuda and pmemd.cuda.MPI links to be relative instead of
> absolute in AMBERHOME/bin directory.
> Updates configure script to optimize for sm35 GPU hardware (Kepler II) in
> cases where cuda v5.0 is detected.
> Makes GTX680 output the gold standard for test cases.
> Fixes incorrect timings that were reported at the end of a run with REMD
> runs in pmemd.
> --------
>
> but it seems that this bugfix was not uploaded to the given server as
> after the attempt
> to click on the given link I have obtained this err.
>
> ------
> Not Found
>
> The requested URL /bugfixes/12.0/bugfix.18 was not found on this server.
>
> Apache/2.2.3 (CentOS) Server at ambermd.org Port 80
> ------
>
> So I assume that this bugfix was still not uploaded and will be soon, am I
> right ?
>
> Best wishes,
>
> Marek
>
>
>
>
>
>
>
>
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jun 01 2013 - 13:30:02 PDT
