[gmx-users] GROMACS 2018 second beta

[Mark Abraham]

Hi GROMACS users,

The second beta release of GROMACS 2018 is available! (We know it's only
2017 right now, but by the time we make the real release it will be almost
2018, so that seems like a good idea!)

We are making this available to you to get an early taste of how GROMACS
2018 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 really need you to test your kinds of
simulation on your hardware, both for correctness and performance. This is
particularly important if you are using "interesting" hardware or
compilers, because we can't test all of them!

We've fixed a number of minor issues that users and developers identified -
please do try out the new version to see if you agree that things have been
fixed where we think they have. No major issues have been identified, which
is very good news. See the release notes for details.

Please do not use this version for doing science you plan to publish - it
needs more testing before it’s reliable enough for that. Similarly, please
don’t use this version as a base for a project that bundles or forks
GROMACS.

What new things can you expect? (See the release notes for more details.)
* support for PME running on a GPU
* improvements for performance of the short-ranged scheme, particularly on
GPUs, through optimizing the pair-list handling
* support for the AWH adaptive biasing scheme
* new simulation quality checks on physical properties of the integrator
* CPU-side enhancements from adding some or better SIMD support to several
computations
* more reporting of conserved quantities for integrators

Just so you know, a fair bit of the work done since 2016 has been
re-organizational, rather than new features or faster performance.

There’s lots of other new things, and a few old things removed - please see
the link to the release notes. All the content of GROMACS 2016.4 (plus
several yet-to-be-released bug fixes) is present, apart from features that
have been removed.

If all goes to plan, we hope to ship the final 2018 release in time for the
New Year, but that relies on people joining in and helping us test! We hope
you will consider making that contribution, so that we can continue to
deliver high-quality free simulation software that will be useful to you on
January 1.

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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018-beta2.tar.gz
Documentation: http://manual.gromacs.org/documentation/2018-beta2/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2018-beta2/ReleaseNotes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2018-beta2.tar.gz

Happy testing!

Mark Abraham
GROMACS Development Manager
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Re: [gmx-users] Gromacs 2018b1: Computing PME on GPUs

[Szilárd Páll]

If you had a previously balanced CPU-GPU setup, expect at max ~25%
improvement (with a decently fast >=Maxwell GPU) and at least a mid-sized
simulation system. GPUs are not great at doing small PME grid work and the
GROMACS PME code is really _fast_, so with small inputs and many/fast CPU
cores (<20-40k, depends on the GPU too!) you will often get better
performance with nonbonded-only offload (or only the FFTs, see the docs for
the mixed mode).

Where the new PME offload shows a large benefit is in cases where you'd
otherwise be strongly CPU-bound by only offloading non-bondeds. In these
cases, you can get up to 1.5-3x improvement. The new offload mode aims to
deliver in _most_ cases >80-90% of the performance you'd previously got
with a decently fast single-socket + GPU by using only 2-4 cores per GPU
(i.e. allowing to run in throughput mode with >=2-3 GPUs per socket).



More concretely, I'll throw in a few examples below (off the top of my
head, so not written in stone!; the official final release will come with
some performance recommendations (so please check those out for
benchmarks).

- given 2xXeon 2640v4 with, say 2x1080 Ti, you can now plug in two more
GPUs and about double the aggregate ns/day per node.
- given a (slightly older) 6-core Haswell i7 5930x with a GTX 980Ti,
depending on your sim system you can plug in 1-2 more cards (say two more
1070s) and get ~2.5-3x of the aggregate ns/day.
- If you have a 4C desktop machine, say with an i7 7600K + 1080, you can
plug in a second GPU.

- However if you had a sever with, say 2x2630v3 + 2xtesla K80, even though
that's only ~4 low-end Haswell cores, Kepler and earlier cards aren't too
fast, so you'r better off running PME on the CPUs.
- Same goes for small simulation systems on balanced machines with decent
amount of CPU cores, keeping PME on the CPU will occasionally be beneficial.


Remember to always read the docs, understand how to use the new features,
and test performance on your system!

Cheers,
--
Szilárd

On Mon, Dec 11, 2017 at 7:30 AM, Alex  wrote:

> Sorry, I am unable to respond to your question, but could you please
> comment on performance difference with and without PME on GPU?
>
> Thanks,
>
> Alex
>
>
> On 12/10/2017 10:28 PM, Jernej Zidar wrote:
>
>> Hi,
>>
>> I’ve been testing the first beta of the upcoming Gromacs 2018, where one
>> of
>> the main features is the ability to run compute PME on GPUs. I tried it
>> and
>> it runs well.
>>
>> My question is: Would it make sense to get a bitcoin mining rig (4,5
>> Nvidia
>> cards, slow CPU) to run simulations in place of the typical dual Xeon
>> workstation with CUDA cards?
>>
>> Thanks!
>>
>> Jernej
>>
>
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[gmx-users] [MGMS-DS]: Molecular Modelling Workshop March 12-14, 2018 in Erlangen, Germany

[Harald Lanig]

Dear list subscribers,

we are very happy to announce next year’s “32nd Molecular Modelling 
Workshop (MMWS)” (http://mmws2018.mgms-ds.de) that takes place on March, 
Monday 12th to Wednesday 14th, 2018, at the 
Friedrich-Alexander-University in Erlangen.


The MMWS has a long history of giving young scientists (especially 
graduate students) the opportunity to present their work and dive into 
discussions with each other and the “older experts” of the field to gain 
valuable feedback from academic as well as industrial colleagues. Oral 
and poster contributions are welcome from all areas of molecular 
modelling – from the life sciences, computational biology and chemistry, 
cheminformatics, to materials sciences.


Starting with the scientific program on Monday after lunch should allow 
to avoid travelling on weekend keeping the expenses at a minimum. A 
hearty workshop dinner and a traditional joint evening in Erlangen’s 
Steinbach-Bräu brewery complement the scientific program. The workshop 
is organised by the German Section of the Molecular Graphics and 
Modelling Society (MGMS-DS e.V.).


### Pre-conference workshop ###
For the first time at our Molecular Modeling Workshop, Schrödinger is 
offering a pre-conference workshop entiteled "Structure-based Drug 
Design using the Schrödinger Suite". If you are interested in 
participating at the software session, please checkmark the 
corresponding field upon filling the registration form.


### Plenary Speakers ###
We are very happy to announce that four outstanding researchers accepted 
our invitation to present a plenary lecture at the workshop:


Bernd Engels (Institute of Physical and Theoretical Chemistry, 
University of Würzburg)

 "Towards the Rational Design of Covalent Inhibitors"

Pavel Hobza (Institute of Organic Chemistry and Biochemistry of the 
Czech Academy of Sciences, Prague)

 "Protein-Ligand Interactions and Drug Design"

Gerhard Wolber (Institute of Pharmacy, Free University of Berlin)
 "Exploring Protein - Ligand Binding Using 3D Pharmacophore Patterns"

Marc Hamm (Henkel AG & Co. KGaA)
 "Facets of Materials Modelling at Henkel"

### Poster and Lecture Awards ###
As in the past years, there will be two poster awards of EUR 100 each 
and three lecture awards for the best contributed oral presentations:


1st winner: Travel bursary to attend the Young Modeller's Forum in 
London, UK, plus a speaker slot option at YMF (travel expenses are 
reimbursed up to EUR 500)


2nd winner: EUR 200 travel expenses reimbursement

3rd winner: EUR 100 travel expenses reimbursement

Only undergraduate and graduate research students qualify for the poster 
and lecture awards.


### Registration and poster/talk submission ###
Submit talks and/or poster titles via the registration form accessible 
on the workshop website https://mmws2018.mgms-ds.de/index.php?m=register

The deadline for all submissions is February 16th, 2018.

### General information ###
Website http://mmws2018.mgms-ds.de will provide all necessary 
information about the meeting.


We are looking forward to meeting you in Erlangen!
- Achim Zielesny, Scientific Committee Workshop Organisation 2018
- Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.org)

--

 PD Dr. Harald Lanig   Universitaet Erlangen/Nuernberg
 Zentralinstitut fuer Scientific Computing (ZISC)
 Geschaeftsfuehrer Martensstrasse 5a, 91058 Erlangen

 Fon   +49 9131-85 20781   harald.la...@fau.de
 Fax   +49 9131-85 20785   http://www.zisc.uni-erlangen.de

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[gmx-users] gmx sasa

[Sudip Das]

Dear All,

I am using 'gmx_mpi sasa' module as below:

gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q
surface.pdb -surface -b 5

Now, surface.pdb file will generate the surface of the selected portion
together with the coordinates of all the atoms present in the protein. Are
the coordinates of all atoms of the protein averaged over the selected
range of trajectory or they are averaged over the range of trajectory
supplied in the .xtc file (as for example, here, I have selected 50-100 ns,
though my .xtc file ranges from 0-100 ns)?
‌
Thanks in advanced!

Best wishes,
Sudip
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Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

[P C Kroon]

I also have good experiences here. It’s even pretty straightforward to compile 
it. The only downside I’ve found so far is that it seems to be impossible to 
get GPU acceleration.

Peter

From: A. Alamir
Sent: 11 December 2017 05:15
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem


Thanks for your feedback.

Abbas

From: Dan Gil
Sent: Saturday, December 9, 2017 5:43 PM
To: gmx-us...@gromacs.org
Cc: 
gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Installing gromacs on the windows 10 linux subsystem

Yes! I have gromacs installed and running on my machine.

Dan

On Sat, Dec 9, 2017 at 4:02 AM A. Alamir  wrote:

> Dear all,
>
> I would like to know if using gromacs on the Windows 10 ubuntu Linux
> subsystem (WLS) is supported. On WLS the gromacs package can be directly
> installed via the Ubuntu apt-get command. I know there are other
> windows-based alternatives to installing/using gromacs (ex. Cygwin), but on
> WLS it is straightforward, providing access to an almost native-like Linux
> experience.
>
> I have noticed that Amber MD can be installed/used on WLS (see
> http://ambermd.org/amber_install.html). Please let me know if you’ve
> successfully tested this for gromacs.
>
> Cheers,
>
> Abbas
>
>
>
>
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