Your message dated Mon, 23 Sep 2013 17:04:07 +0000
with message-id <[email protected]>
and subject line Bug#706608: fixed in cp2k 2.4.0-1
has caused the Debian Bug report #706608,
regarding cp2k: wrong amber torsion energy
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
706608: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=706608
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: cp2k
Version: 2.2.426-1
Severity: normal
Tags: upstream,patch
A bug has been found in the AMBER force field topology input regarding
torsion energies. It has been fixed in upstream revision 12867.
Michael
On Thu, May 02, 2013 at 11:18:03AM +0200, Teodoro Laino wrote:
> Thanks Letif and apologies for the delay.
>
> The issue was indeed a bug and the fix is in the SVN. Should you
> encounter other discrepancies, please, do not hesitate to report them.
> best,
>
> Teo
>
> On Apr 22, 2013, at 8:54 PM, Letif Mones <[email protected]> wrote:
>
> > Hi Teo,
> >
> > I am sending the following files: amber and cp2k inputs, amber
> > restart file and amber topology file (dmpoh_vacuum.atop). I also
> > attached another topology file (dmpoh_vacuum_mod.atop) in which I
> > halved the dihedral force constants. With this latter cp2k gives the
> > right answer.
> >
> > Regards,
> >
> > Letif
> >
> >
> >
> >
> > On 22 Apr 2013, at 17:53, Teodoro Laino wrote:
> >
> >> Dear Letif,
> >>
> >> thanks for reporting this issue. All parameters should be converted
> >> at the moment they are read. We also had few examples to check the
> >> numerics and I remember they were matching with Sander they were
> >> OK. Do you have an input file (including all relevant files) that
> >> shows this problem?
> >>
> >> Thanks,
> >> Teo
> >>
> >> On Apr 22, 2013, at 5:23 PM, Letif Mones <[email protected]> wrote:
> >>
> >>> Hi,
> >>>
> >>> I did a molecular mechanical calculation in cp2k using an amber
> >>> topology file (force field: amber99). When I checked the bonded
> >>> energy terms I found that the bond and angle terms are correct but
> >>> the dihedral energy is twice as the energy calculated by sander. I
> >>> think the reason is that in the amber FF the form of the torsion
> >>> potential is: K / 2 * [ 1 + cos[ M*PHI - PHI0 ] ] while cp2k uses
> >>> the form of K * [ 1 + cos[ M*PHI - PHI0 ] ]. So should not the
> >>> torsion force constant read from an amber topology file be
> >>> multiplied by 0.5 (and the improper one too as it has the same
> >>> form)?
> >>>
> >>> Letif
--- End Message ---
--- Begin Message ---
Source: cp2k
Source-Version: 2.4.0-1
We believe that the bug you reported is fixed in the latest version of
cp2k, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael Banck <[email protected]> (supplier of updated cp2k package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Mon, 23 Sep 2013 11:39:02 +0200
Source: cp2k
Binary: cp2k cp2k-data
Architecture: source amd64 all
Version: 2.4.0-1
Distribution: unstable
Urgency: low
Maintainer: Michael Banck <[email protected]>
Changed-By: Michael Banck <[email protected]>
Description:
cp2k - Ab Initio Molecular Dynamics
cp2k-data - Ab Initio Molecular Dynamics (data files)
Closes: 706608
Changes:
cp2k (2.4.0-1) unstable; urgency=low
.
* New upstream release.
+ Fixes AMBER torsion energy (Closes: #706608)
* New features include:
+ Resolution-of-the-identity RI-MP2 and RI-RPA energies
+ Non-local vDW corrections for XC functionals including B88-vDW, PBE-vDW
and B97X-D
+ Various new XC functionals via LibXC support
+ Support for non-linear core corrected (NLCC) pseudopotentials
+ Adaptive QM/MM
+ Additional linear scaling algorithms and properties
+ ELPA parallel eigensolver support
+ Possibility of using image charges
+ Integrated basis set optimisation
+ PLUMED support
.
[ Daniel Leidert ]
* debian/control (DM-Upload-Allowed): Dropped.
(Standards-Version): Bumped to 3.9.4.
(Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical.
* debian/watch: Fixed.
* debian/patches/fftw3_unaligned.patch: Dropped (applied upstream).
* debian/patches/dftb_atom_input_dependence.patch: Ditto.
* debian/patches/series: Adjusted.
.
[ Michael Banck ]
* debian/rules (override_dh_auto_test): Update OMPI_MCA environment variable
to orte_rsh_agent as the original plm_rsh_agent variable is deprecated.
* debian/control (Build-Depends): Added libxc-dev.
* debian/patches/makeflags.patch: Added support for libxc.
* debian/rules (override_dh_auto_test): Added QS/regtest-libxc to
testsuite directories.
* debian/cp2k-data.install: Install all data files from tests/QS directory.
* debian/patches/basis_set_error_631++Gxx.patch: Dropped (applied upstream).
* debian/patches/gcc-4.8_fixes.patch: Likewise.
* debian/cp2k.install: Moved documentation to ...
* debian/cp2k-data.install: ... here.
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cp2k_2.4.0-1.debian.tar.gz
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