Mark Abraham | 5 Dec 20:22 2013
Picon

GROMACS 5.0-beta1 is released!

Hi GROMACS users,

The first beta release of GROMACS 5.0 is available! We are making this available to you to get an early taste of how GROMACS 5.0 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of GROMACS as high as possible, we’re human, we overlook things while doing other things, and we need your many pairs of eyes to help build a tool that we can all use to do good science! We’d love it if you could try this new version of GROMACS out on the kinds of work that you do, and let us know what you think - good and bad! Please do not use this version for doing science you plan to publish - it needs more testing before it’s reliable enough for that.


What new things can you expect? Here’s some of the big changes already present:

* GROMACS now uses a combination of C++98 and C99, so you will need a working C++ compiler that is intended to work with your C compiler

* Building GROMACS now requires CMake version 2.8.8, which will mean some of you will need to update your version in order to build GROMACS. We don’t like needing to get you to do that, but that’s the price of letting the GROMACS developers focus more on writing code for reliable and fast MD simulations, rather than maintaining a build system that works with 12 different feature sets of CMake 2.8.x

* GROMACS tools are now bundled together into just two binaries - mdrun and gmx. The latter contains most of the tools familiar to you, perhaps with new names, and a couple of new ones. For the time being, the install procedure will also create symbolic links so that your old scripts will keep working for a time, but these will go away at some future point

* A handful of the tools have been re-implemented using a new C++ analysis framework, which we hope will provide a better platform for maintaining and adding to their functionality in the future.

* The Verlet cut-off scheme is now the default in GROMACS. One of our design principles is that GROMACS will do correct simulations by default, and the use of this scheme makes that easy and fast. In the long term, the group cut-off scheme will be removed, but there is not yet a timetable for that.

* You can now treat Lennard-Jones interactions with PME, which is expected to provide a much better treatment of spatially heterogeneous long-ranged dispersion interactions at cost comparable to that of a cutoff. The implementation is still being enhanced, so for now neither free-energy calculations nor the Verlet cut-off scheme works with it, but we plan to finish those off soon.

* Enhanced testing suite, with unit tests for most new C++ code.


There’s lots of other new things, and old things removed - please see the link to the release notes below for more details. All the content of GROMACS 4.6.5 is present, apart from features that have been removed.


There’s quite a few other shiny features the hard-working GROMACS developers are still polishing, including supporting the few remaining algorithms missing from the Verlet cut-off scheme, adding support for Intel Xeon Phi, adding support for the new efficient TNG trajectory-file format, and more. If those sound interesting to you, please take a look at the work in progress at http://gerrit.gromacs.org - early testers and reviewers of code are always welcome!


If all goes to plan, we hope to ship the final 5.0 release in early February, but that relies on people joining in and helping us test! We hope you will consider making that contribution, so we we can continue to deliver high-quality free simulation software.


You can find the code, manual, release notes, installation instructions and test
suite at the links below.

ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz

ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf

http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1

http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0

http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz


Happy testing!


Mark

GROMACS development manager
_______________________________________________
Announcements from the Gromacs team
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-announce
Alexey Shvetsov | 5 Dec 21:22 2013
Picon

Re: GROMACS 5.0-beta1 is released!

Hi Mark!

Genbox segfaults in beta1 and git master

http://redmine.gromacs.org/issues/1393

Mark Abraham писал 05-12-2013 23:22:
> Hi GROMACS users,
> 
> The first beta release of GROMACS 5.0 is available! We are making this
> available to you to get an early taste of how GROMACS 5.0 will look and
> work, and most importantly to get feedback from you about how well 
> things
> work. While we try our hardest to keep the quality of GROMACS as high 
> as
> possible, we’re human, we overlook things while doing other things, and 
> we
> need your many pairs of eyes to help build a tool that we can all use 
> to do
> good science! We’d love it if you could try this new version of GROMACS 
> out
> on the kinds of work that you do, and let us know what you think - good 
> and
> bad! Please do not use this version for doing science you plan to 
> publish -
> it needs more testing before it’s reliable enough for that.
> 
> 
> What new things can you expect? Here’s some of the big changes already
> present:
> 
> * GROMACS now uses a combination of *C++98* and C99, so you will need a
> working C++ compiler that is intended to work with your C compiler
> 
> * Building GROMACS now requires *CMake version 2.8.8*, which will mean 
> some
> of you will need to update your version in order to build GROMACS. We 
> don’t
> like needing to get you to do that, but that’s the price of letting the
> GROMACS developers focus more on writing code for reliable and fast MD
> simulations, rather than maintaining a build system that works with 12
> different feature sets of CMake 2.8.x
> 
> * GROMACS tools are now bundled together into *just two binaries* - 
> mdrun
> and gmx. The latter contains most of the tools familiar to you, perhaps
> with new names, and a couple of new ones. For the time being, the 
> install
> procedure will also create symbolic links so that your old scripts will
> keep working for a time, but these will go away at some future point
> 
> * A handful of the tools have been re-implemented using a* new C++ 
> analysis
> framework*, which we hope will provide a better platform for 
> maintaining
> and adding to their functionality in the future.
> 
> * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
> design principles is that GROMACS will do correct simulations by 
> default,
> and the use of this scheme makes that easy and fast. In the long term, 
> the
> group cut-off scheme will be removed, but there is not yet a timetable 
> for
> that.
> 
> * You can now treat *Lennard-Jones interactions with PME*, which is
> expected to provide a much better treatment of spatially heterogeneous
> long-ranged dispersion interactions at cost comparable to that of a 
> cutoff.
> The implementation is still being enhanced, so for now neither 
> free-energy
> calculations nor the Verlet cut-off scheme works with it, but we plan 
> to
> finish those off soon.
> 
> * Enhanced testing suite, with *unit tests* for most new C++ code.
> 
> There’s lots of other new things, and old things removed - please see 
> the
> link to the release notes below for more details. All the content of
> GROMACS 4.6.5 is present, apart from features that have been removed.
> 
> There’s quite a few other shiny features the hard-working GROMACS
> developers are still polishing, including supporting the few remaining
> algorithms missing from the Verlet cut-off scheme, adding support for 
> Intel
> Xeon Phi, adding support for the new efficient TNG trajectory-file 
> format,
> and more. If those sound interesting to you, please take a look at the 
> work
> in progress at http://gerrit.gromacs.org - early testers and reviewers 
> of
> code are always welcome!
> 
> If all goes to plan, we hope to ship the final 5.0 release in early
> February, but that relies on people joining in and helping us test! We 
> hope
> you will consider making that contribution, so we we can continue to
> deliver high-quality free simulation software.
> 
> 
> You can find the code, manual, release notes, installation instructions 
> and
> test
> suite at the links below.
> 
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz
> 
> ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf
> 
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1
> 
> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
> 
> http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz
> 
> Happy testing!
> 
> Mark
> GROMACS development manager

-- 
Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 
Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum <at> gmail.com
mailto:alexxy <at> gentoo.org
mailto:alexxy <at> omrb.pnpi.spb.ru
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Gianluca Interlandi | 6 Dec 01:07 2013

Re: GROMACS 5.0-beta1 is released!

Dear Mark,

Does GROMACS 5.0 have the ability to perform Monte Carlo steps?

Thanks,

      Gianluca

On Thu, 5 Dec 2013, Mark Abraham wrote:

> Hi GROMACS users,
>
> The first beta release of GROMACS 5.0 is available! We are making this
> available to you to get an early taste of how GROMACS 5.0 will look and
> work, and most importantly to get feedback from you about how well things
> work. While we try our hardest to keep the quality of GROMACS as high as
> possible, we?re human, we overlook things while doing other things, and we
> need your many pairs of eyes to help build a tool that we can all use to do
> good science! We?d love it if you could try this new version of GROMACS out
> on the kinds of work that you do, and let us know what you think - good and
> bad! Please do not use this version for doing science you plan to publish -
> it needs more testing before it?s reliable enough for that.
>
>
> What new things can you expect? Here?s some of the big changes already
> present:
>
> * GROMACS now uses a combination of *C++98* and C99, so you will need a
> working C++ compiler that is intended to work with your C compiler
>
> * Building GROMACS now requires *CMake version 2.8.8*, which will mean some
> of you will need to update your version in order to build GROMACS. We don?t
> like needing to get you to do that, but that?s the price of letting the
> GROMACS developers focus more on writing code for reliable and fast MD
> simulations, rather than maintaining a build system that works with 12
> different feature sets of CMake 2.8.x
>
> * GROMACS tools are now bundled together into *just two binaries* - mdrun
> and gmx. The latter contains most of the tools familiar to you, perhaps
> with new names, and a couple of new ones. For the time being, the install
> procedure will also create symbolic links so that your old scripts will
> keep working for a time, but these will go away at some future point
>
> * A handful of the tools have been re-implemented using a* new C++ analysis
> framework*, which we hope will provide a better platform for maintaining
> and adding to their functionality in the future.
>
> * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
> design principles is that GROMACS will do correct simulations by default,
> and the use of this scheme makes that easy and fast. In the long term, the
> group cut-off scheme will be removed, but there is not yet a timetable for
> that.
>
> * You can now treat *Lennard-Jones interactions with PME*, which is
> expected to provide a much better treatment of spatially heterogeneous
> long-ranged dispersion interactions at cost comparable to that of a cutoff.
> The implementation is still being enhanced, so for now neither free-energy
> calculations nor the Verlet cut-off scheme works with it, but we plan to
> finish those off soon.
>
> * Enhanced testing suite, with *unit tests* for most new C++ code.
>
> There?s lots of other new things, and old things removed - please see the
> link to the release notes below for more details. All the content of
> GROMACS 4.6.5 is present, apart from features that have been removed.
>
> There?s quite a few other shiny features the hard-working GROMACS
> developers are still polishing, including supporting the few remaining
> algorithms missing from the Verlet cut-off scheme, adding support for Intel
> Xeon Phi, adding support for the new efficient TNG trajectory-file format,
> and more. If those sound interesting to you, please take a look at the work
> in progress at http://gerrit.gromacs.org - early testers and reviewers of
> code are always welcome!
>
> If all goes to plan, we hope to ship the final 5.0 release in early
> February, but that relies on people joining in and helping us test! We hope
> you will consider making that contribution, so we we can continue to
> deliver high-quality free simulation software.
>
>
> You can find the code, manual, release notes, installation instructions and
> test
> suite at the links below.
>
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz
>
> ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1
>
> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
>
> http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz
>
> Happy testing!
>
> Mark
> GROMACS development manager
> -- 
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@...
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca <at> u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
                     http://healthynaturalbaby.org
-----------------------------------------------------
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Michael Shirts | 6 Dec 01:46 2013
Picon

Re: GROMACS 5.0-beta1 is released!

Unfortunately, that isn't going to make it into 5.0.  It is very
definitely on the plan soon after that, though.

On Thu, Dec 5, 2013 at 7:07 PM, Gianluca Interlandi
<gianluca <at> u.washington.edu> wrote:
> Dear Mark,
>
> Does GROMACS 5.0 have the ability to perform Monte Carlo steps?
>
> Thanks,
>
>      Gianluca
>
>
> On Thu, 5 Dec 2013, Mark Abraham wrote:
>
>> Hi GROMACS users,
>>
>> The first beta release of GROMACS 5.0 is available! We are making this
>> available to you to get an early taste of how GROMACS 5.0 will look and
>> work, and most importantly to get feedback from you about how well things
>> work. While we try our hardest to keep the quality of GROMACS as high as
>> possible, we?re human, we overlook things while doing other things, and we
>>
>> need your many pairs of eyes to help build a tool that we can all use to
>> do
>> good science! We?d love it if you could try this new version of GROMACS
>> out
>>
>> on the kinds of work that you do, and let us know what you think - good
>> and
>> bad! Please do not use this version for doing science you plan to publish
>> -
>> it needs more testing before it?s reliable enough for that.
>>
>>
>> What new things can you expect? Here?s some of the big changes already
>>
>> present:
>>
>> * GROMACS now uses a combination of *C++98* and C99, so you will need a
>> working C++ compiler that is intended to work with your C compiler
>>
>> * Building GROMACS now requires *CMake version 2.8.8*, which will mean
>> some
>> of you will need to update your version in order to build GROMACS. We
>> don?t
>> like needing to get you to do that, but that?s the price of letting the
>>
>> GROMACS developers focus more on writing code for reliable and fast MD
>> simulations, rather than maintaining a build system that works with 12
>> different feature sets of CMake 2.8.x
>>
>> * GROMACS tools are now bundled together into *just two binaries* - mdrun
>> and gmx. The latter contains most of the tools familiar to you, perhaps
>> with new names, and a couple of new ones. For the time being, the install
>> procedure will also create symbolic links so that your old scripts will
>> keep working for a time, but these will go away at some future point
>>
>> * A handful of the tools have been re-implemented using a* new C++
>> analysis
>> framework*, which we hope will provide a better platform for maintaining
>> and adding to their functionality in the future.
>>
>> * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
>> design principles is that GROMACS will do correct simulations by default,
>> and the use of this scheme makes that easy and fast. In the long term, the
>> group cut-off scheme will be removed, but there is not yet a timetable for
>> that.
>>
>> * You can now treat *Lennard-Jones interactions with PME*, which is
>> expected to provide a much better treatment of spatially heterogeneous
>> long-ranged dispersion interactions at cost comparable to that of a
>> cutoff.
>> The implementation is still being enhanced, so for now neither free-energy
>> calculations nor the Verlet cut-off scheme works with it, but we plan to
>> finish those off soon.
>>
>> * Enhanced testing suite, with *unit tests* for most new C++ code.
>>
>> There?s lots of other new things, and old things removed - please see the
>>
>> link to the release notes below for more details. All the content of
>> GROMACS 4.6.5 is present, apart from features that have been removed.
>>
>> There?s quite a few other shiny features the hard-working GROMACS
>>
>> developers are still polishing, including supporting the few remaining
>> algorithms missing from the Verlet cut-off scheme, adding support for
>> Intel
>> Xeon Phi, adding support for the new efficient TNG trajectory-file format,
>> and more. If those sound interesting to you, please take a look at the
>> work
>> in progress at http://gerrit.gromacs.org - early testers and reviewers of
>> code are always welcome!
>>
>> If all goes to plan, we hope to ship the final 5.0 release in early
>> February, but that relies on people joining in and helping us test! We
>> hope
>> you will consider making that contribution, so we we can continue to
>> deliver high-quality free simulation software.
>>
>>
>> You can find the code, manual, release notes, installation instructions
>> and
>> test
>> suite at the links below.
>>
>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz
>>
>> ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf
>>
>>
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1
>>
>> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
>>
>> http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz
>>
>> Happy testing!
>>
>> Mark
>> GROMACS development manager
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
>> a mail to gmx-users-request@...
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca <at> u.washington.edu
>                     +1 (206) 685 4435
>                     http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
>                     http://healthynaturalbaby.org
> -----------------------------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request@...
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Yorquant Wang | 6 Dec 07:37 2013
Picon

Re: GROMACS 5.0-beta1 is released!

Hi Mark!
    Does the new released GMX5.0.x surpport AXV2.0 instruction set? You
know, MD simulations involve many integer calculations,and AVX2 instruction set
which widens the Integer register to 256 bit can greetly speed up the
simulation.

best,
cheers

Yorquant Wang
SJTU
Shanghai China

2013/12/6 Mark Abraham <mark.j.abraham@...>

> Hi GROMACS users,
>
> The first beta release of GROMACS 5.0 is available! We are making this
> available to you to get an early taste of how GROMACS 5.0 will look and
> work, and most importantly to get feedback from you about how well things
> work. While we try our hardest to keep the quality of GROMACS as high as
> possible, we’re human, we overlook things while doing other things, and we
> need your many pairs of eyes to help build a tool that we can all use to do
> good science! We’d love it if you could try this new version of GROMACS out
> on the kinds of work that you do, and let us know what you think - good and
> bad! Please do not use this version for doing science you plan to publish -
> it needs more testing before it’s reliable enough for that.
>
>
> What new things can you expect? Here’s some of the big changes already
> present:
>
> * GROMACS now uses a combination of *C++98* and C99, so you will need a
> working C++ compiler that is intended to work with your C compiler
>
> * Building GROMACS now requires *CMake version 2.8.8*, which will mean some
> of you will need to update your version in order to build GROMACS. We don’t
> like needing to get you to do that, but that’s the price of letting the
> GROMACS developers focus more on writing code for reliable and fast MD
> simulations, rather than maintaining a build system that works with 12
> different feature sets of CMake 2.8.x
>
> * GROMACS tools are now bundled together into *just two binaries* - mdrun
> and gmx. The latter contains most of the tools familiar to you, perhaps
> with new names, and a couple of new ones. For the time being, the install
> procedure will also create symbolic links so that your old scripts will
> keep working for a time, but these will go away at some future point
>
> * A handful of the tools have been re-implemented using a* new C++ analysis
> framework*, which we hope will provide a better platform for maintaining
> and adding to their functionality in the future.
>
> * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
> design principles is that GROMACS will do correct simulations by default,
> and the use of this scheme makes that easy and fast. In the long term, the
> group cut-off scheme will be removed, but there is not yet a timetable for
> that.
>
> * You can now treat *Lennard-Jones interactions with PME*, which is
> expected to provide a much better treatment of spatially heterogeneous
> long-ranged dispersion interactions at cost comparable to that of a cutoff.
> The implementation is still being enhanced, so for now neither free-energy
> calculations nor the Verlet cut-off scheme works with it, but we plan to
> finish those off soon.
>
> * Enhanced testing suite, with *unit tests* for most new C++ code.
>
> There’s lots of other new things, and old things removed - please see the
> link to the release notes below for more details. All the content of
> GROMACS 4.6.5 is present, apart from features that have been removed.
>
> There’s quite a few other shiny features the hard-working GROMACS
> developers are still polishing, including supporting the few remaining
> algorithms missing from the Verlet cut-off scheme, adding support for Intel
> Xeon Phi, adding support for the new efficient TNG trajectory-file format,
> and more. If those sound interesting to you, please take a look at the work
> in progress at http://gerrit.gromacs.org - early testers and reviewers of
> code are always welcome!
>
> If all goes to plan, we hope to ship the final 5.0 release in early
> February, but that relies on people joining in and helping us test! We hope
> you will consider making that contribution, so we we can continue to
> deliver high-quality free simulation software.
>
>
> You can find the code, manual, release notes, installation instructions and
> test
> suite at the links below.
>
> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz
>
> ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf
>
>
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1
>
> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
>
> http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz
>
> Happy testing!
>
> Mark
> GROMACS development manager
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request@...
>

-- 
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai
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Szilárd Páll | 6 Dec 08:09 2013
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Re: GROMACS 5.0-beta1 is released!

On Fri, Dec 6, 2013 at 7:37 AM, Yorquant Wang <wangykoo@...> wrote:
> Hi Mark!
>     Does the new released GMX5.0.x surpport AXV2.0 instruction set? You
> know, MD simulations involve many integer calculations,and AVX2 instruction set
> which widens the Integer register to 256 bit can greetly speed up the
> simulation.

No, it was planned, but it did not make it.

--
Szilárd

>
> best,
> cheers
>
> Yorquant Wang
> SJTU
> Shanghai China
>
>
>
> 2013/12/6 Mark Abraham <mark.j.abraham@...>
>
>> Hi GROMACS users,
>>
>> The first beta release of GROMACS 5.0 is available! We are making this
>> available to you to get an early taste of how GROMACS 5.0 will look and
>> work, and most importantly to get feedback from you about how well things
>> work. While we try our hardest to keep the quality of GROMACS as high as
>> possible, we’re human, we overlook things while doing other things, and we
>> need your many pairs of eyes to help build a tool that we can all use to do
>> good science! We’d love it if you could try this new version of GROMACS out
>> on the kinds of work that you do, and let us know what you think - good and
>> bad! Please do not use this version for doing science you plan to publish -
>> it needs more testing before it’s reliable enough for that.
>>
>>
>> What new things can you expect? Here’s some of the big changes already
>> present:
>>
>> * GROMACS now uses a combination of *C++98* and C99, so you will need a
>> working C++ compiler that is intended to work with your C compiler
>>
>> * Building GROMACS now requires *CMake version 2.8.8*, which will mean some
>> of you will need to update your version in order to build GROMACS. We don’t
>> like needing to get you to do that, but that’s the price of letting the
>> GROMACS developers focus more on writing code for reliable and fast MD
>> simulations, rather than maintaining a build system that works with 12
>> different feature sets of CMake 2.8.x
>>
>> * GROMACS tools are now bundled together into *just two binaries* - mdrun
>> and gmx. The latter contains most of the tools familiar to you, perhaps
>> with new names, and a couple of new ones. For the time being, the install
>> procedure will also create symbolic links so that your old scripts will
>> keep working for a time, but these will go away at some future point
>>
>> * A handful of the tools have been re-implemented using a* new C++ analysis
>> framework*, which we hope will provide a better platform for maintaining
>> and adding to their functionality in the future.
>>
>> * The *Verlet cut-off scheme is now the default* in GROMACS. One of our
>> design principles is that GROMACS will do correct simulations by default,
>> and the use of this scheme makes that easy and fast. In the long term, the
>> group cut-off scheme will be removed, but there is not yet a timetable for
>> that.
>>
>> * You can now treat *Lennard-Jones interactions with PME*, which is
>> expected to provide a much better treatment of spatially heterogeneous
>> long-ranged dispersion interactions at cost comparable to that of a cutoff.
>> The implementation is still being enhanced, so for now neither free-energy
>> calculations nor the Verlet cut-off scheme works with it, but we plan to
>> finish those off soon.
>>
>> * Enhanced testing suite, with *unit tests* for most new C++ code.
>>
>> There’s lots of other new things, and old things removed - please see the
>> link to the release notes below for more details. All the content of
>> GROMACS 4.6.5 is present, apart from features that have been removed.
>>
>> There’s quite a few other shiny features the hard-working GROMACS
>> developers are still polishing, including supporting the few remaining
>> algorithms missing from the Verlet cut-off scheme, adding support for Intel
>> Xeon Phi, adding support for the new efficient TNG trajectory-file format,
>> and more. If those sound interesting to you, please take a look at the work
>> in progress at http://gerrit.gromacs.org - early testers and reviewers of
>> code are always welcome!
>>
>> If all goes to plan, we hope to ship the final 5.0 release in early
>> February, but that relies on people joining in and helping us test! We hope
>> you will consider making that contribution, so we we can continue to
>> deliver high-quality free simulation software.
>>
>>
>> You can find the code, manual, release notes, installation instructions and
>> test
>> suite at the links below.
>>
>> ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0-beta1.tar.gz
>>
>> ftp://ftp.gromacs.org/pub/manual/manual-5.0-beta1.pdf
>>
>>
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0-beta1
>>
>> http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0
>>
>> http://gromacs.googlecode.com/files/regressiontests-5.0-beta1.tar.gz
>>
>> Happy testing!
>>
>> Mark
>> GROMACS development manager
>> --
>> Gromacs Users mailing list
>>
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>>
>
>
>
> --
> Yukun Wang
> PhD candidate
> Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> Tong University
> Cell phone: 13621806236.
> China Shanghai
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Ricardo O. S. Soares | 6 Dec 12:49 2013
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Re: GROMACS 5.0-beta1 is released!

Hello Mark, thanks for the news. 

I couldn't find this info on the release notes, but let me ask you anyway, has bug #1166 (from g_order) been
corrected? 

Thanks, 

Ricardo Soares. 

--- 
Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
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David van der Spoel | 6 Dec 13:25 2013
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Re: GROMACS 5.0-beta1 is released!

On 2013-12-06 12:49, Ricardo O. S. Soares wrote:
> Hello Mark, thanks for the news.
>
> I couldn't find this info on the release notes, but let me ask you anyway, has bug #1166 (from g_order) been corrected?
>
As you can see on redmine http://redmine.gromacs.org/issues/1166 the 
answer unfortunately is no.

> Thanks,
>
> Ricardo Soares.
>
> ---
> Biological Chemistry and Physics
> Faculty of Pharmaceutical Sciences at Ribeirão Preto
> University of São Paulo - Brazil
>

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel <at> xray.bmc.uu.se    http://folding.bmc.uu.se
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Ricardo O. S. Soares | 6 Dec 17:16 2013
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Re: GROMACS 5.0-beta1 is released!

I see, 

thanks David. 

--- 
Biological Chemistry and Physics 
Faculty of Pharmaceutical Sciences at Ribeirão Preto 
University of São Paulo - Brazil 
----- Mensagem original -----

> De: "David van der Spoel" <spoel <at> xray.bmc.uu.se>
> Para: gmx-users <at> gromacs.org
> Enviadas: Sexta-feira, 6 de Dezembro de 2013 10:25:05
> Assunto: Re: [gmx-users] GROMACS 5.0-beta1 is released!

> On 2013-12-06 12:49, Ricardo O. S. Soares wrote:
> > Hello Mark, thanks for the news.
> >
> > I couldn't find this info on the release notes, but let me ask you
> > anyway, has bug #1166 (from g_order) been corrected?
> >
> As you can see on redmine http://redmine.gromacs.org/issues/1166 the
> answer unfortunately is no.

> > Thanks,
> >
> > Ricardo Soares.
> >
> > ---
> > Biological Chemistry and Physics
> > Faculty of Pharmaceutical Sciences at Ribeirão Preto
> > University of São Paulo - Brazil
> >

> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel <at> xray.bmc.uu.se http://folding.bmc.uu.se
> --
> Gromacs Users mailing list

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Gmane