Re: [gmx-users] Regarding MD simulations involving metal ion (Mn)

[Paul bauer]

Hello,

for metal ions (and especially transition metals) you should first 
consider what kind of metal model you want to employ, as the different 
models (bonded, soft sphere or dummy model) have have different properties.
There are numerous papers outlining the parametrization of those 
different models, so you can search them once you have decided on how 
you want to model the ion :)


If you are in need of modelling things such as unpaired electrons, spin 
effects or anything else quantum mechanical, you should consider if MD 
is the correct approach to simulate a structure like this or if a pure 
QM description is more appropriate.


If you have a reference for a similar system you should follow the 
approach outlined there as much as possible.


Also one note of caution, you should only use one force field to 
simulate your system, and never mix and match force fields.


Cheers

Paul

On 16/05/18 11:57, dhaval patel wrote:

Dear All,

I need to simulation of protein-ligand with coordinated metal ion bound to
ligand. The metal ion is Mn+2, Advise me whether its correct to use
CHARMM36 and OPLSS force field for parameterization? What things should
taken care while simulating such cases where we have metals with unpaired
electrons?   Any help is  highly appreciated.



Sincerely yours,
​Dhaval​



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Re: [gmx-users] Specbond.dat file

[Paul Bauer]

Hej,

the specbond.dat file is for extra bonds between non-neighbouring 
residues (e.g. disulphide bridges).


So if you don't need to add anything extra for your residue there if it 
doesn't do anything like a disulphide would.


Cheers

Paul


On 2018-05-22 09:24, Hemalatha Jayabal wrote:

Hi all,

I have added a residue (Hydroxyproline) to my .rtp files and have updated
the hdb and ffbonded files. While browsing through the manual about
specbond.dat, it says that any "special bonds" are to be listed
specifically here. Does this mean for the newly added residue also, the
bond connections are to be added? (Irrespective of whether it is forming a
basic head to tail inter residue bonds with the other standard residues
preceding and following it). If so, is it safe to use the distance between
the atoms (that forms inter residue bonds) from protein structure and use
it in the "length" factor in specbond.dat?

Thank you all in advance

Best Regards
Hemalatha


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Re: [gmx-users] Error while compiling GROMACS 2018

[Paul Bauer]

Hello,

it seems like you have some manually copied files in your source tree. 
Please try to remove them and build again.
The line you see in the first error message was changed during the 
recent testing (listed-forces/bonded.cpp) and is causing the error in 
your local copy (listed-forces/bonded_2.cpp).


Cheers

Paul

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Re: [gmx-users] constant pressure in NPT simulation

[Paul bauer]

Hello,

what do you mean with the pressure not being constant? If you mean the 
fluctuations in the instantaneous pressure, this is normal. What should 
be constant is the time average of the pressure over the time of the 
simulation.
I don't see anything particular in your mdp file that could cause the 
pressure coupling to fail.


Cheers

Paul

On 03/08/18 09:14, Lucia Mydlova wrote:

Dear all customers.

I have a problem, in my NPT simulations the pressure is not constant and
the temperature is. Earlier simulation in NVT conditions was ok. I use
these parameters:
  tcoupl  =  nose-hoover
tc_grps =  system
tau_t   =  0.002
ref_t   =  500
Pcoupl  =  parrinello-rahman
pcoupltype  =  isotropic
tau_p   =  1.0
compressibility =  4.5e-5
ref_p   =  1.0

What should I change in the .mpd file?
Thank you very much.
Lucia



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Re: [gmx-users] Overlapping frames within one .xtc

[Paul bauer]

Hello,

if you restart a run from the checkpoint file than any recent version of 
GROMACS will make sure that there are no overlapping frames and that the 
continuation is exact.
What were you trying to do on the command line when you wanted to 
continue the run, and what version have you been using?


Cheers

Paul

On 15/08/18 10:43, Sergio Perez wrote:

Dear GMX comunity,

I would like to know if a run is interrupted abruptly (killed by the user)
and then is restarted with -append option, is there any chance that
overlapping frames are generated within the .xtc file?

If this were to happen, would
  gmx trjcat -f trj.xtc -o trj2.xtc -overwrite

solve the problem?

Thank you all very much in advance!

Best,

Sergio Pérez-Conesa



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Re: [gmx-users] Feedback wanted - mdp option for preparation vs production

[Paul bauer]

To add my 2 cents to the discussion, I think having the explicit switch 
between preparation and production runs will be definitely useful for 
users, and I think it will also make it easier to rework the input 
settings if we can simply have one check at the beginning that 
determines if we are harsh in denying the use of options or not. As an 
additional bonus, I think mdrun could decide based on this setting if it 
is more bold in stating if options are wrong or not, something that gets 
lost when people just default to use maxwarn as an option for grompp to 
make errors go away.


Cheers

Paul

On 24/08/2018 15:26, Justin Lemkul wrote:



On 8/24/18 9:09 AM, Mark Abraham wrote:

Hi,

You can't prevent misuse... give someone a scalpel and they might lose a
finger! The key targets for helping are the newer users who don't 
have the
experience to know which way to hold the scalpel. If they can be 
trained to

use these flags (e.g. because they see them in their tutorials) then the
warnings can have the intended effect. One can mitigate the impact of
someone always running in the least safe mode by reporting on that to 
the
log file, so that they'll see it, and so will their collaborators, or 
their

peers when they archive and share their results.


I also think there's value in having a user go into an .mdp file and 
set "stage = preparation" because now they (presumably) know that what 
they are doing is applying an algorithm that is intended for a 
preparatory process. If we require a user to simply add -maxwarn 1 to 
their grompp command, the user begins to think "yeah, that's how I can 
make that error go away." The former requires scientific thought, the 
latter emboldens carelessness.


For those wondering the backstory, I started a Redmine at 
https://redmine.gromacs.org/issues/2622 because I felt we were a bit 
harsh in making the use of Berendsen a warning, because we also 
caution users against using Parrinello-Rahman for equilibration. So if 
one shouldn't use Parrinello-Rahman and *can't* use Berendsen, what 
conclusion is the user to make about performing equilibration? In this 
case, it's acceptable to use Berendsen, if and only if the user 
acknowledges that the resulting ensembles are wrong and therefore 
should not be collected as real data.


-Justin


Mark

On Fri, Aug 24, 2018 at 2:48 PM Victor Rosas Garcia 


wrote:

El jue., 23 ago. 2018 a las 17:03, Mark Abraham 
(
)

escribió:


Hi,

[snip, snip]
Despite this, there are times when one might want to use such an

algorithm,

and so we permit users to suppress warnings from grompp with -maxwarn.
However, encouraging such behaviour leads to people abusing 
-maxwarn, and

we'd all like to avoid that.

[snip, snip]
Following discussion among some developers, how do people feel about a

new

mdp option that permits users to specify e.g. "production" or
"preparation," defaulting to "production." grompp retains its current
warning behaviour for "production," but merely advises about such 
issues
when preparing systems. Do those names and behaviours seem 
suitable? Do

we

need more flavours of calculation type?

Hello Mark,

First of all, thanks for all the time and effort you put into these
matters.

Regarding these new flavours of calculation, how will these new 
flavours
prevent abuse?  If people are abusing -maxwarn, what will keep these 
same
people from using always "preparation" to suppress the warnings?  
GROMACS

is a great program but in the end, it boils down to the fundamental
question "do you want to do a good job or a bad job?" I'm all for 
getting
clearer error messages and more complete warnings (sometimes I have 
learned

from them).

just my 2 cents

Victor
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[gmx-users] GROMACS 2018.3 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2018.3 is available!

This release fixes several issues found since 2018.2. We encourage all 
users of the 2018

series to update to 2018.3. Please see the link to the release notes below
for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.3.tar.gz
Documentation: http://manual.gromacs.org/documentation/2018.3/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.3.tar.gz

Happy simulating!

Paul Bauer
GROMACS Release Manager

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Re: [gmx-users] Gromacs 2018.3 install warning

[Paul bauer]

Hello,

we have not yet full support for gcc-8, but this is being worked on. You 
can disregard those warnings safely for now.


/Paul

On 29/08/2018 14:01, Du, Yu wrote:

Dear gmx-users,




I was installing gromacs-2018.3 with gcc8.1, `make -j 24` gave the following 
warning:


`make check` with regression test set 100% passed. Hope next version will fix 
these warnings.


##Warnings##
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:
 In function ‘void make_benchmark_tprs(const char*, char**, gmx_int64_t, 
gmx_int64_t, real, real, real, int*, t_inputinfo*, FILE*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:21:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
  std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
  
^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_tune_pme.cpp:1080:63:
 note: length computed here
  std::strncpy(fn_bench_tprs[j], fn_sim_tpr, 
std::strlen(fn_sim_tpr)-std::strlen(".tpr"));
 ~~~^~~~
[ 33%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o


[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o
In function ‘void calc_cumulatives(t_UmbrellaWindow*, int, t_UmbrellaOptions*, 
const char*, const char*)’,
 inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1689:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
  sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));
  
~~~^~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1274:74:
 note: length computed here
  sprintf(fn, "%s_cumul.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4));

~~~^~~~
In function ‘void print_histograms(const char*, t_UmbrellaWindow*, int, int, 
t_UmbrellaOptions*, const char*)’,
 inlined from ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’ at 
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1735:29:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:16:
 warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends 
on the length of the source argument [-Wstringop-overflow=]
  sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
  
~~~^~~
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:
 In function ‘void do_bootstrapping(const char*, const char*, const char*, 
const char*, char*, double*, t_UmbrellaWindow*, int, t_UmbrellaOptions*)’:
/share/home/para008/software_new/src/gromacs-2018.3/src/gromacs/gmxana/gmx_wham.cpp:1516:73:
 note: length computed here
  sprintf(fn, "%s_bs%d.xvg", std::strncpy(buf, fnhist, 
std::strlen(fnhist)-4), bs_index);
   
~~~^~~~
[ 35%] Building CXX object 
src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o
##Warnings##



--
Du, Yu
PhD Student,
Shanghai Institute of Organic Chemistry
345 Ling Ling Rd., Shanghai, China.
Zip: 200032, Tel: (86) 021 5492 5275



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Re: [gmx-users] force field parameters for Fe3O4?

[Paul bauer]

Hello,

I would recommend that you check relevant publications for the 
simulation of magnetite if people have tried to simulate it in solvent.
I could not find anything during a short search, but maybe you'll be 
more successful. :)
If there are no published parameters in the literature you will have to 
parametrize the molecule yourself according to the method used by the 
force field you are using.
I would look at the section in the user guide dealing with this 
(http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields) 
and then at the documentation for your force field!


Cheers!

On 13/04/18 11:21, leila karami wrote:

Dear gromacs users,

I want to simulate a protein in different concentration of Fe3O4.

How to obtain force field parameters of Fe3O4?

Any help will highly be appreciated.

Best,



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Re: [gmx-users] force field parameters for Fe3O4?

[Paul bauer]

Hello,

this depends on the force field you are using. Some of them use 
parameters from a QM optimization and partial charge calculation.
But even then you need to be careful that the results from the QM are 
not just random numbers :)


But I'm not sure myself how I would tackle something like Magnetite 
right now, as it would also require obtaining parameters for the LJ 
interactions.


Cheers!

On 13/04/18 12:13, rose rahmani wrote:

On Fri, 13 Apr 2018, 14:35 Paul bauer, <paul.baue...@gmail.com> wrote:


Hello,

I would recommend that you check relevant publications for the
simulation of magnetite if people have tried to simulate it in solvent.
I could not find anything during a short search, but maybe you'll be
more successful. :)
If there are no published parameters in the literature you will have to
parametrize the molecule yourself according to the method used by the
force field you are using.
I would look at the section in the user guide dealing with this
(
http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields)



Is it true to optimize the molecule for example in gaussian(dft)first, and
then calculate the charges and make an .itp file for it?is it always
reliable?


and then at the documentation for your force field!

Cheers!

On 13/04/18 11:21, leila karami wrote:

Dear gromacs users,

I want to simulate a protein in different concentration of Fe3O4.

How to obtain force field parameters of Fe3O4?

Any help will highly be appreciated.

Best,


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Re: [gmx-users] trjconv ndec not working

[Paul Bauer]

Hello Eric,

I had a look at the code for writing gro files and it looks to me that 
it is only able to write three decimal places there.
There is a comment in the code that mentions that writing other 
precisions has been removed.

This means that we need to update the man page text to not be confusing.

Cheers

Paul


On 2018-04-15 17:45, Eric Smoll wrote:

Hello Joe,

Thanks for the reply. Sorry if I was not clear. I provide a gro file with high 
precision (7 decimal places). For some reason, the output gro always has three 
decimal places. The manual   for trjconv suggests that the output should have 7 
decimal places.

Best,
Eric


On Apr 15, 2018, at 4:00 AM, Joe Jordan  wrote:

Are you trying to write from an xtc file? If so, does it have the necessary
precision?


On Sun, Apr 15, 2018 at 4:53 AM, Eric Smoll  wrote:

Hello Gromacs Users,

I am using Gromacs 2018.1.

The manual page for gmx trjconv states the number of decimal places in the
output of a gro file is taken from the number of decimal places in the
input unless the ndec flag is set. The ndec flag can be used to increase
precision in the output.

However, providing trjconv a gro file with increased coordinate precision
(7 decimal places) does not increase the precision of the output gro file.
Also, the ndec flag has no impact on the output precision.

My input gro is written as follows:

comment
10
1ABC C11  -0.1204914  -0.0759159  -0.0131147
...etc.

trconv does not complain about this file format and creates a normal, three
decimal
gro file as output.

Has this feature been removed?

Best,
Eric
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Re: [gmx-users] source code for velocity information

[Paul bauer]

Hello,

in newer versions of Gromacs you can generate documentation from the 
comments in the code using Doxygen.
This is then build and included in a local copy of the html 
documentation when running `make  webpage`, or `make doxygen-all`
You can then navigate the code documentation there or at the official 
site for the current version 
(http://manual.gromacs.org/documentation/current/index.html).
I would still highly recommend using something more recent than 5.x, as 
those versions have also left maintenance now.
You could try either the 2016 or 2018 releases, both of them are 
officially supported right now.


/Paul

On 21/03/18 09:36, 刘杰 wrote:

hellow Joe JordanSo glad to  receive your adcives, I have installed 
gromacs5.1.1, and useing  gromacs for three years , but I know little about  a 
newer version you can use the automatically generated function documentation as 
you said , could you give more details about this. any help will be appreciate.


Liu Jie



在 2018-03-21 15:39:41，"Joe Jordan"  写道：

A few suggestions:if you use a newer version you can use the automatically 
generated

function documentation to find what you want

*use a newer version of gromacs; 4.x is no longer supported with bug fixes >*use find or grep to find what you want >*if you use a newer version you can use the automatically generated >function documentation to find what you want 
> >On Wed, Mar 21, 2018 at 2:44 AM, 刘杰  wrote: > >> Dear all, Iam trying to add viscidity bond code to gromacsc 4.0.7. I >> found the harmonic bond code in bondfree.c ,but i could not conform 
which >> source document include the velocity information . Can somebody please >> advise me on how to overcome this issue?Thank you. Regards, jieliu >> -- >> 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-requ...@gromacs.org. >> > > > >-- >Joe Jordan >-- >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 
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[gmx-users] First beta release of 2019

[Paul bauer]

Hi GROMACS users,

The first beta release of GROMACS 2019 is available!

We are making this available to you to get an early taste of how GROMACS
2019 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!

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 update groups to reduce communication overhead
* support for offloading PME long range interactions to single GPU using 
OpenCL

* support for Intel integrated GPUs with OpenCL

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2018.3
is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2019 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-2019-beta1.tar.gz
Documentation: http://manual.gromacs.org/documentation/2019-beta1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2019-beta1.tar.gz

Happy testing!

Paul Bauer
GROMACS release manager

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Re: [gmx-users] First beta release of 2019

[Paul bauer]

Hello GROMACS users,

the correct link to the release notes is here:

http://manual.gromacs.org/documentation/2019-beta1/release-notes/index.html

Cheers

Paul Bauer
GROMACS Release manager

On 22/10/2018 17:29, Paul bauer wrote:

Hi GROMACS users,

The first beta release of GROMACS 2019 is available!

We are making this available to you to get an early taste of how GROMACS
2019 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!

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 update groups to reduce communication overhead
* support for offloading PME long range interactions to single GPU 
using OpenCL

* support for Intel integrated GPUs with OpenCL

There’s lots of other new things, and a few old things removed - 
please see
the release notes for the complete list. All the content of GROMACS 
2018.3

is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2019 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-2019-beta1.tar.gz
Documentation: 
http://manual.gromacs.org/documentation/2019-beta1/index.html

(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2019-beta1.tar.gz

Happy testing!

Paul Bauer
GROMACS release manager



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Re: [gmx-users] Error in writing trajectory files using HPC (vGromacs 2018.2)

[Paul bauer]

Hello,

could you open an issue on redmine.gromacs.org to describe the problem, 
with the commands you used and if possible some example files (not full 
length trajectories, but the minimal file that causes the crash).

The same goes for the gmx helix issue you ran into.

Cheers

Paul

On 16/10/2018 16:08, Budheswar Dehury wrote:

Dear All,

I am going through very bad phase while analyzing huge trajectories (23 GB, 
POPC membrane protein systems: Atoms: 201382) using HPC system installed at HPC 
facility of Denmark Technical University, Denmark. I have checked the 
trajectory, which seems fine with the gmx check command...

Though it reads the trajectories but while writing the compressed forms after 
reading all the frames, it shows the following error..

*** Error in `gmx': munmap_chunk(): invalid pointer: 0x7f76c609386e ***
=== Backtrace: =
/lib64/libc.so.6(+0x7f574)[0x7f76c3fa6574]
/appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(_Z8done_topP10t_topology+0x39)[0x7f76c5263f59]
/appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(gmx_trjconv+0x1a3a)[0x7f76c54e6ffa]
/appl/gromacs/2018.2/XeonE5-2680v2/bin/../lib64/libgromacs.so.3(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x261)[0x7f76c5143ca1]
gmx[0x40e58c]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f76c3f493d5]
gmx[0x40e651]
=== Memory map: 
0040-0043f000 r-xp  00:bb 70350544   
/appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
0063e000-0063f000 r--p 0003e000 00:bb 70350544   
/appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
0063f000-0064 rw-p 0003f000 00:bb 70350544   
/appl/gromacs/2018.2/XeonE5-2680v2/bin/gmx
01506000-01d83000 rw-p  00:00 0  [heap]
7f76c1ca5000-7f76c1ce3000 r-xp  00:bb 64559031   
/appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0
7f76c1ce3000-7f76c1ee3000 ---p 0003e000 00:bb 64559031   
/appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0
7f76c1ee3000-7f76c1ee4000 rw-p 0003e000 00:bb 64559031   
/appl/gcc/7.3.0/lib64/libquadmath.so.0.0.0
7f76c1ee4000-7f76c2003000 r-xp  08:05 518663 
/usr/lib64/libgfortran.so.3.0.0
7f76c2003000-7f76c2203000 ---p 0011f000 08:05 518663 
/usr/lib64/libgfortran.so.3.0.0
7f76c2203000-7f76c2204000 r--p 0011f000 08:05 518663 
/usr/lib64/libgfortran.so.3.0.0
7f76c2204000-7f76c2206000 rw-p 0012 08:05 518663 
/usr/lib64/libgfortran.so.3.0.0
7f76c2206000-7f76c220f000 r-xp  08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c220f000-7f76c240e000 ---p 9000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c240e000-7f76c240f000 r--p 8000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c240f000-7f76c241 rw-p 9000 08:05 516182 
/usr/lib64/libltdl.so.7.3.0
7f76c241-7f76c241a000 r-xp  08:05 515617 
/usr/lib64/libnuma.so.1
7f76c241a000-7f76c261a000 ---p a000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261a000-7f76c261b000 r--p a000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261b000-7f76c261c000 rw-p b000 08:05 515617 
/usr/lib64/libnuma.so.1
7f76c261c000-7f76c31c5000 r-xp  00:bb 31025797   
/appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so
7f76c31c5000-7f76c33c5000 ---p 00ba9000 00:bb 31025797   
/appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so
7f76c33c5000-7f76c33d3000 rw-p 00ba9000 00:bb 31025797   
/appl/OpenBLAS/0.2.14/XeonE5-2680v2/gcc/lib/libopenblas-r0.2.14.so
7f76c33d3000-7f76c34e2000 rw-p  00:00 0
7f76c34e2000-7f76c36d r-xp  00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c36d-7f76c38cf000 ---p 001ee000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38cf000-7f76c38e r--p 001ed000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38e-7f76c38e1000 rw-p 001fe000 00:bb 70339951   
/appl/fftw/3.3.8/XeonE5-2680v2/gcc-7.3.0/lib/libfftw3f.so.3.5.8
7f76c38e1000-7f76c38e8000 r-xp  08:05 515140 
/usr/lib64/librt-2.17.so
7f76c38e8000-7f76c3ae7000 ---p 7000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae7000-7f76c3ae8000 r--p 6000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae8000-7f76c3ae9000 rw-p 7000 08:05 515140 
/usr/lib64/librt-2.17.so
7f76c3ae9000-7f76c3aeb000 r-xp  08:05 515116 
/usr/lib64/libdl-2.17.so
7f76c3aeb000-7f76c3ceb000 ---p 2000 08:05 515116 
/usr/lib64/libdl-2.17.so

Re: [gmx-users] start the simulation of the last stopping point.

[Paul Bauer]

Hello,

you can find information on how to extend simulations here:
http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html

Cheers

Paul

On 2018-11-08 14:23, Edjan Silva wrote:

Dear fellow scientists,

I'm doing a 40ns simulation between DNA and a small molecule. It occurred
that around 30 nanoseconds, the computer hung up.

How do I start the simulation from the 30 nanoseconds performed?

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[gmx-users] GROMACS 2018.4 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2018.4 is available!

This release fixes several issues found since 2018.3. We encourage all 
users of the 2018

series to update to 2018.4. Please see the link to the release notes below
for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.4.tar.gz
Documentation: http://manual.gromacs.org/documentation/2018.4/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.4.tar.gz

Happy simulating!

Paul Bauer
GROMACS Release Manager

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[gmx-users] Second beta release of GROMACS 2019

[Paul bauer]

Hi GROMACS users,

The second beta release of GROMACS 2019 is now out and available!

As before, we are making the testing versions available for you to be 
able to get feedback
on how well things are working, and what could be improved or if there 
are any bugs

in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, 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 update groups to reduce communication overhead
* support for offloading PME long range interactions to single GPU using 
OpenCL

* support for Intel integrated GPUs with OpenCL

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2018.3
is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2019 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.

There is another beta release planned for the end of November, as well
as at least one release candidate in December.

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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019-beta2.tar.gz
Documentation: 
http://manual.gromacs.org/documentation/2019-beta2/index.html

(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2019-beta2/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2019-beta2.tar.gz

Happy testing!

Paul Bauer
GROMACS release manager

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[gmx-users] GROMACS 2019 official release

[Paul bauer]

The official release of GROMACS 2019 is now available.

What new things can you expect? Please see the release notes highlights at
http://manual.gromacs.org/2019/release-notes/index.html.

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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.tar.gz
Documentation: http://manual.gromacs.org/2019/index.html
(includes install guide, user guide, reference manual, and release notes)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.tar.gz

Happy simulating!

--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] GROMACS 2018.5 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2018.5 is available!

This release fixes several issues found since 2018.4. We encourage all 
users of the 2018

series to update to 2018.5. Please see the link to the release notes below
for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.5.tar.gz
Documentation: http://manual.gromacs.org/2018.5/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.5.tar.gz

Happy simulating!

Paul

--

Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] Make errors 2019rc1

[Paul bauer]

Hello,

I just confirmed this, and opened an issue on Redmine 
(https://redmine.gromacs.org/issues/2809).
I guess we will try to fix it and roll a different release candidate 
after that.


Thanks for reporting the issue!

Paul

On 14/12/2018 20:53, Raymond Arter wrote:

Paul,

The CMake and system configuration are:

OS:   Scientific Linux 6.6
CPU: Intel(R) Xeon(R) CPU E5-2630 v2 @ 2.60GHz
RAM: 32829272 kB

python = 2.7.10
cuda = 9.2.148
gcc = 7.3.0
cmake = 3.9.0
binutils = 2.31

Nvidia driver version: 396.37
GPU: 4x Tesla K10.G2.8GB

cmake .. -DGMX_BUILD_OWN_FFTW=ON
 -DGMX_DOUBLE=OFF
 -DGMX_OPENMP=ON
 -DGMX_GPU=ON
 -DCUDA_TOOLKIT_ROOT_DIR=/opt/apps/libs/cuda/9.2.148
 -DGMX_SIMD=AVX_256
-DCMAKE_INSTALL_PREFIX=/opt/apps/general/gromacs/2019rc1/float/gcc/7.3.0/cuda/9.2.148 


 -DREGRESSIONTEST_DOWNLOAD=ON

Thanks for the quick reply.

Kind regards,

Ray




On 14/12/2018 17:37, Paul Bauer wrote:

Hello,

Can you send your CMake command and system configuration?

Cheers

Paul

On Fri, 14 Dec 2018, 18:27 Raymond Arter 
Hi,

I'm seeing the following errors at the end of the make step:

[100%] Linking CXX executable ../../bin/template
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_destroy(gmx_fft*)'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_init_1d(gmx_fft**, int, int)'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_init_1d_real(gmx_fft**, int, int)'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_2d_real(gmx_fft*, gmx_fft_direction, 
void*,

void*)'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_init_2d_real(gmx_fft**, int, int, int)'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_1d(gmx_fft*, gmx_fft_direction, void*,
void*)'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_cleanup()'
/opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
undefined reference to `gmx_fft_1d_real(gmx_fft*, gmx_fft_direction, 
void*,

void*)'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/template] Error 1
make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
make: *** [all] Error 2

I'm compiling Gromacs in the same way as 2019beta2 and 3, and I 
didn't see

these errors.
Am I making a silly mistake or is it something else?

Regards.
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[gmx-users] GROMACS 2019 release candidate

[Paul bauer]

Hi GROMACS users,

The GROMACS 2019 release candidate is now out and available!

As before, we are making the testing versions available for you to be 
able to get feedback
on how well things are working, and what could be improved or if there 
are any bugs

in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, please do not use this version for doing science you plan to 
publish -
even though it should be stable now, we still want to use the last weeks 
to iron out

any remaining issues that might show up. 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 update groups to reduce communication overhead
* Support for offloading PME long range interactions to single GPU using 
OpenCL


There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2018.4
is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2019 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-2019-rc1.tar.gz
Documentation: http://manual.gromacs.org/2019-rc1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/2019-rc1/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2019-rc1.tar.gz

Happy testing!

Paul Bauer
GROMACS release manager


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Re: [gmx-users] Make errors 2019rc1

[Paul Bauer]

Hello,

Can you send your CMake command and system configuration?

Cheers

Paul

On Fri, 14 Dec 2018, 18:27 Raymond Arter  Hi,
>
> I'm seeing the following errors at the end of the make step:
>
> [100%] Linking CXX executable ../../bin/template
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_destroy(gmx_fft*)'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_init_1d(gmx_fft**, int, int)'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_init_1d_real(gmx_fft**, int, int)'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_2d_real(gmx_fft*, gmx_fft_direction, void*,
> void*)'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_init_2d_real(gmx_fft**, int, int, int)'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_1d(gmx_fft*, gmx_fft_direction, void*,
> void*)'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_cleanup()'
> /opt/apps/general/binutils/2.31/bin/ld: ../../lib/libgromacs.so.4.0.0:
> undefined reference to `gmx_fft_1d_real(gmx_fft*, gmx_fft_direction, void*,
> void*)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [bin/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make: *** [all] Error 2
>
> I'm compiling Gromacs in the same way as 2019beta2 and 3, and I didn't see
> these errors.
> Am I making a silly mistake or is it something else?
>
> Regards.
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Re: [gmx-users] Running Grompp in reverse and backing up MD data

[Paul bauer]

Hello,

just a warning concerning the last message: The mdp from gmx dump -om 
will not be the complete representation of your tpr, and you will not be 
able to regenerate the tpr from this mdp file! I have been working on a 
variant that would make this possible, but so far have not managed it.


Cheers
Paul

On 29/11/2018 16:53, Thomas Piggot wrote:

You can get an mdp from a tpr using gmx dump -om

Cheers

Tom

On 29/11/2018 14:58, Peter Kroon wrote:

Hi all,


thanks for all the feedback.

@Milan: I've made a tally of diskspace used per filetype in our lab. In
general people here don't save trr files at all (too expensive), yet
still out of 125TB total, 65% is made up of xtc files, and 10% is trr
files (followed by gro and xvg at 2.5% each). And that kind of backup
space becomes expensive. Of course for some simulations that were super
expensive to run we should back up the trajectories. But as a general
solution it's impossible. That also opens up the point of tiered
backups. For example: archive for the past 5 years to verify old
research results; off-site backups for the past 3 months in case the
building burns down; and local storage against accidental deletion. For
each there are different requirements and costs.

@Mark: Part of the reason for this discussion is figuring out what my
responsibility is exactly. My thought was that as the TPR in general
contains the same information as the input used to make it, at least a
partial reverse should be possible. Then again, mdp/top/itp files are
pretty small (17GB/35GB/110GB respectively) and should be very
compressible. By comparison, tprs make up 880GB here.

@Justin: Great point, thanks!


Thanks guys :)


Peter


On 29-11-18 15:29, Mark Abraham wrote:

Hi,

Yes, that's useful output, though strictly some mdp settings (like
constraints and gen-vel) are consumed by grompp and thus not 
reported there.


Mark

On Thu, Nov 29, 2018 at 3:16 PM Justin Lemkul  wrote:


On 11/29/18 6:43 AM, Peter Kroon wrote:

Hi Mark,

thanks for the rapid reply!

Hmmn. It doesn't have to be exactly matching input. An equivalent to
e.g. mdout.mdp produced by grompp would already be good enough for my

All of the input .mdp settings are also written to the header of the
.log file for the run.

-Justin

purposes. The same goes for a top file containing only the 
interactions

relevant to the system.


Peter

On 29-11-18 11:31, Mark Abraham wrote:

Hi,

Unfortunately there is no way to generate matching inputs to grompp

from a
.tpr file. In the longer term, we want that to be possible, but 
it will
require a total rework of how users specify inputs, and that's a 
large

effort!

Mark

On Thu, Nov 29, 2018 at 11:27 AM Peter Kroon  
wrote:



Hi all,


In the lab we're thinking about backup solutions for MD data 
(and in
particular gromacs produced data). Since trajectories tend to be 
large

we quickly decided that backing up the results of simulations is a

waste
of disk space. Instead, we'll probably go for backing up the TPR 
files.


Now for the question: Is there an easy way of generating the 
files used
to generate the TPR files? For example the MDP file used to make 
a TPR
file? How about a top file (I assume the original split between 
top and
itp is lost)? I know I can get the starting configuration (gro) 
using

editconf.

And does anyone here have any other blinding insights on backing 
up MD

data?


Cheers,

Peter


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==

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Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129

[gmx-users] Third beta release of GROMACS 2019

[Paul bauer]

Hi GROMACS users,

The third beta release of GROMACS 2019 is now out and available!

As before, we are making the testing versions available for you to be 
able to get feedback
on how well things are working, and what could be improved or if there 
are any bugs

in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, 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 update groups to reduce communication overhead
* support for offloading PME long range interactions to single GPU using 
OpenCL

* support for Intel integrated GPUs with OpenCL

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2018.4
is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2019 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.

The plan is now to have one release candidate released in December before
the final release in January 2019.

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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019-beta3.tar.gz
Documentation: http://manual.gromacs.org/documentation/2019-beta3/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2019-beta3/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2019-beta3.tar.gz

Happy testing!

Paul Bauer
GROMACS release manager

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Re: [gmx-users] Bond breakage modelling

[Paul Bauer]

Hello,

in general I would advise not to use a classical force field to model a 
quantum mechanical effect like breaking a bond.
Classical force fields are not parametrized to reproduce those effects, 
and while you might get something that looks fine with the morse 
potential it would definitely be unphysical.
If you want to study quantum effects, use a QM method for the parts that 
are involved in bond breaking, or use a reactive force field like ReaxFF.


Cheers

Paul

On 2019-02-19 13:35, Ali Khodayari wrote:

Dear Peter,

Thank you for your prompt reply.
I think I can try the morse potential to see how the system responds.
Could you kindly provide some more info about how to implement it?
Best regards,
Ali




On 19 Feb 2019, at 11:35, Peter Kroon  wrote:

Hi Ali,


The short answer is "not really". You could model your bonds as
non-bonded (morse) potentials, but then you lose all angle dependence on
the potential energy, since the non-bonded potentials must be pair-wise.
Depending on the exact problem this may be acceptable though. The angle
dependence on the potential energy also immediately points out an issue
with your cut-off based approach: how will you deal with the angle(s)?

In literature I have seen some papers of people pulling proteins apart,
breaking cystein bridges. Those may contain some insight/ideas.


Peter


On 19-02-19 11:28, Ali Khodayari wrote:
Dear All,



We have simulated a cellulose fiber using GLYCAM06 ff parameters converted
to GROMACS. The model is validated and works properly.

We are investigating the behavior of the material under tensile load.
However, as covalent bonds are modelled with a harmonic potential -as it is
in most of the non-reactive force fields- some parameters cannot be
extracted. Is there any way to mimic the breakage of the bonds, let's say
when the distance of the atoms exceed a certain amount? In other words, if
we have a rough idea of the strain at which bonds break, can GROMACS neglect
bonds from a certain cut-off onwards?

Thank you in advanced for your responses.

Kind regards,

Ali


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[gmx-users] GROMACS 2018.6 patch release available

[Paul bauer]

Hi GROMACS users,

I just released another patch release of GROMACS 2018, bringing the 
official version to 2018.6!


We decided to release this additional patch due to issues found in 
2018.5 that could affect scientific correctness, so we encourage all 
users of the 2018
series to update to 2018.6. Please see the link to the release notes 
below for more details.
The 2018 branch continues to be in support only for issues that affect 
scientific issues, while the 2019 branch is under active support.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.6.tar.gz
Documentation: http://manual.gromacs.org/2018.6/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.6.tar.gz

Happy simulating!

Paul

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Re: [gmx-users] CU2+ nonbonded parameteres (sigma and epsilon)

[Paul Bauer]

Hello,

Classical force fields are a bad way to describe the behaviour of
transition metals such as CU2+, because they are not able to cover the
behaviour of the D-orbitals with just the sigma and epsilon parameters.
What are you planning to use the model for? It is possible to parametrize
transition metals for this, but it is a lengthy and time consuming process.

Kindest regards
Paul

On Fri, 15 Mar 2019, 19:53 Mohsen Asadbegi, 
wrote:

> Hi!
>
> I need to add non-bonded CU2+ ion to CHRAMM36. How can I find these
> parameters (sigma and epsilon)? Does it enough to define CU2+ by its
> charge, mass, sigma and epsilon?
> In addition, I want to know that what are the units of sigma and epsilon in
> the CHARMM36 force field?
>
> Regards,
> Mohsen Asadbegi.
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[gmx-users] GROMACS 2016.6 patch release available

[Paul bauer]

Hi GROMACS users,

due to a recently discovered and fixed bug that caused unintended 
behaviour of GROMACS that could result in wrong physical behaviour of
simulated systems, we decided to release one more point release of the 
2016 branch of GROMACS, even though the branch has been official marked

out of support.

The bug affected force-switched LJ interactions only on the GPU, 
normally only used in combination with the CHARMM force field. One possible
observation of the unphysical behaviour would be through apparent 
distortion in membrane systems.


Please note that there have been some additional changes necessary to 
allow this change to pass our verification pipelines, as those had
already been moved past the stage of supporting the 2016 branch. We 
fully intend to support all previously tested configurations for this

branch, even though we had to disable testing for them.

The change itself is not expected to affect any results besides the 
behaviour fixed by the bug itself.
You can find more information about the fixed bug itself in the release 
notes here:


http://manual.gromacs.org/2016.6/ReleaseNotes/index.html

As always, the code, test suite and documentation can be found at the 
links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2016.6.tar.gz
Documentation: http://manual.gromacs.org/documentation/2016.6/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2016.6.tar.gz

Happy simulating!

Paul Bauer

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0046737308594

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[gmx-users] GROMACS 2019.1 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.1 is available!

This first patch release fixes several issues found since the initial 
release of GROMACS 2019. We encourage all users of the 2019

series to update to 2019.1. Please see the link to the release notes below
for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.1.tar.gz
Documentation: http://manual.gromacs.org/2019.1/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.1.tar.gz

Happy simulating!

Paul

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[gmx-users] GROMACS 2019.1 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.2 is available!

This second patch release fixes several issues found since the last 
patch release of GROMACS 2019. We encourage all users of the 2019

series to update to 2019.2. Please see the link to the release notes below
for more details.

You can find the code, documentation, release notes, and test suite at the
links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz
Documentation: http://manual.gromacs.org/2019.2/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.2.tar.gz

Happy simulating!

Paul

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0046737308594

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Re: [gmx-users] GROMACS 2019.2 patch release available

[Paul bauer]

Hello again,

apologies for messing up the subject line, this is of course for the 
2019.2 point release!


Cheers

Paul

On 16/04/2019 13:41, Paul bauer wrote:

Hi GROMACS users,

The official release of GROMACS 2019.2 is available!

This second patch release fixes several issues found since the last 
patch release of GROMACS 2019. We encourage all users of the 2019
series to update to 2019.2. Please see the link to the release notes 
below

for more details.

You can find the code, documentation, release notes, and test suite at 
the

links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.2.tar.gz
Documentation: http://manual.gromacs.org/2019.2/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: 
http://gerrit.gromacs.org/download/regressiontests-2019.2.tar.gz


Happy simulating!

Paul



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0046737308594

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Re: [gmx-users] Segmentation fault, core dumped error

[Paul bauer]

Hello,

can you please open a new issue on redmine.gromacs.org for this, and 
upload your input files (if possible) and the command line you used that 
caused the error?


Thanks

Paul

On 29/05/2019 01:31, Neena Susan Eappen wrote:

Hello gromacs users,

Is there a reason why segmentation fault appeared when gmx hbond command was 
used?

Thank you,
Neena


From: Neena Susan Eappen
Sent: Friday, May 24, 2019 12:40 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

I got an error message when I used gmx hbond command: Segmentation fault, core 
dumped. Shown below is my gmx version details (if that can point to my 
problem). Any insight would be appreciated.

GROMACS version:2018.4
Precision:  single
Memory model:   64 bit
MPI library:thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:disabled
SIMD instructions:  AVX2_256
FFT library:fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:enabled
Hwloc support:  disabled
Tracing support:disabled
Built on:   2019-01-12 0:35
Built by:   name@HP-PC [CMAKE]<mailto:name@HP-PC%20[CMAKE]>
Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
Build CPU vendor:   Intel
Build CPU brand:Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
Build CPU family:   6   Model: 61   Stepping: 4
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt 
intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd 
rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/cc GNU 7.3.0
C compiler flags:   march=core-AVX2 -O3 -DNDEBUG -funroll-all-loops 
-fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags: -march=core-avx2-std=c++11   -O3 -DNDEBUG 
-funroll-all-loops -fexcess-precision=fast

Thank you,
Neena



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[gmx-users] GROMACS 2018.7 patch release available

[Paul bauer]

Hi GROMACS users,

I just released another patch release of GROMACS 2018, bringing the 
official version to 2018.7!


We decided to release this additional patch due to issues found in 
2018.6 that could affect scientific correctness, so we encourage all 
users of the 2018
series to update to 2018.7. Please see the link to the release notes 
below for more details.
The 2018 branch continues to be in support only for issues that affect 
scientific issues, while the 2019 branch is under active support.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.7.tar.gz
Documentation: http://manual.gromacs.org/2018.7/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.7.tar.gz

Happy simulating!

Paul

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0046737308594

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[gmx-users] GROMACS 2019.3 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.3 is available!

This third patch release fixes several issues found since the second 
patch release of GROMACS 2019.

We encourage all users of the 2019 series to update to 2019.3.
Please see the link to the release notes below for more details.

You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.3.tar.gz
Documentation: http://manual.gromacs.org/2019.3/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.3.tar.gz

Happy simulating!

Paul

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0046737308594

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Re: [gmx-users] Grompp not producing tpr files

[Paul Bauer]

Hello,

Yes, the last part indicates an error that should not happen.

Which version did you use to run this?

If it is a version before 2018, can you try the newer versions to see if
the error persists?

Cheers

Paul



On Thu, 13 Jun 2019, 17:04 Israel Estrada,  wrote:

> Thanks for the replies!
>
> Mark, the process seemed to "finish" properly (my terminal did not close,
> and the command line was waiting for the next command as if it ran
> normally). I looked for the output file (ions.tpr) in the working
> directory, or any new files, but nothing was generated.
>
> Bratin, here is what my terminal displayed,
> "command line:
> gmx grompp -f ions.mdp -c box.gro -o ions.tpr -p topol.top
>
> Setting the LD random seed to 973096069
> Segmentation fault (core dumped)"
> The last part seems to be the error, right?
>
> Thanks again!!
> -Israel
>
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Bratin
> Kumar Das <177cy500.bra...@nitk.edu.in>
> Sent: Wednesday, June 12, 2019 7:00:55 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Grompp not producing tpr files
>
> Hi
>Give here the full error
>
> On Thu 13 Jun, 2019, 1:35 AM Mark Abraham, 
> wrote:
>
> > Hi,
> >
> > Was grompp exiting normally, or crashing? Are you looking in the right
> > place, for a file of the right name? :-)
> >
> > Mark
> >
> > On Wed., 12 Jun. 2019, 18:42 Israel Estrada,  wrote:
> >
> > > Hello users,
> > >
> > >
> > > I'm running into problems trying to grompp; I'm using the command
> > >
> > >
> > > gmx grompp -f ions.mdp -c etc_box.gro  -o ions.tpr -p topol.top
> > >
> > >
> > > and the process shows no error messages, but output files are not being
> > > generated. I'm running this on a small molecule, about 20 atoms, with
> the
> > > hopes that I can modify OPLS parameters as needed. I'm sure the problem
> > is
> > > related to an error in the topology files, but I don't know how or if I
> > can
> > > fix this.
> > >
> > >
> > > Any help would be greatly appreciated, thank you!
> > >
> > > -Israel
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > >
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> or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
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> or
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Re: [gmx-users] There is no domain decomposition error

[Paul bauer]

Hello,

did you change the command to submit the calculation or did you use a 
different machine to run the calculations?
This error usually means that the domain decomposition can't run on the 
requested number of (thread)-MPI ranks.


Try using a different number of ranks or different combinations of 
-ntmpi and -ntomp.


Cheers

Paul

On 10/06/2019 07:39, Dhrubajyoti Maji wrote:

Dear gromacs users,
  I am studying a system of molten acetamide in GROMACS-2018.3. I
have run EM and then NPT equilibration of 5 ns. Here-under, everything is
fine but when I try to run a 50 ns NPT production run the following error
occurs :
There is no domain decomposition for 56 ranks that is compatible with the
given box and a minimum cell size of 0.57125 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings.
 I have checked gromacs documentation error and could not find
anything fruitful. The mdp file for equilibration and production are almost
same except for number of steps.
Could you please tell what is going wrong and how to solve it ?
Thanks in advance.
Dhrubajyoti Maji



--
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GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] using GPU acceleration in gromacs

[Paul bauer]

Hello,

the versions of GROMACS that are in the package repositories are not 
recommended for simulations, as most of the hardware specific 
optimizations and GPU support are turned off there.
If you want to use GPU acceleration you'll need to compile GROMACS 
yourself following the instructions found here 
http://manual.gromacs.org/current/install-guide/index.html


Cheers

Paul

On 24/05/2019 08:58, Pragati Sharma wrote:

Hello users,

I am trying to install gromacs-2019 on a HP workstation containing
NVIDIA-quadro 5000 GPU card.

I installed gromacs using ‘sudo apt-get install gromacs’ on opensuse. After
running a polymer simulation, I checked the log file and it is showing
GPU-disabled in Gromacs properties. I need to know, if it is not using GPU
because of the quick installation, or there can be other reasons. Should I
manually reinstall gromacs using cmake with ‘-DGMX GPU=ON’. OR Are there
other things that can be checked or done to make the gromacs use GPU
acceleration.  Any help would be appreciated.



--
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GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] gromacs make check failure

[Paul bauer]

Hello,

from looking at the output from make check it looks like this is 
harmless. The tests simply took longer than the internally set cut-off 
of 30 seconds.
If you are unsure about the build, you can run the test binary manually 
from the build directory with (./gmxpreprocess-test in the same 
directory where you can find the gmx binary).

Then it won't use the cut-off and will take as much time as it will need.

Cheers

Paul

On 20/05/2019 16:26, Nelson Chris AWE wrote:

Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and OpenMPI

When I run make check, I get a failure on test 29:

29 - GmxPreprocessTests (Timeout)

Any advice would be much appreciated.

Links to output files:

   1.  Build environment 
(https://drive.google.com/open?id=1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ks )
   2.  Build output 
(https://drive.google.com/open?id=1PQFllv49M-Op6HLtdKsRJfwHbFeEsint )
   3.  Dependency list 
(https://drive.google.com/open?id=13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7T )
   4.  Make checkout output 
(https://drive.google.com/open?id=1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1 )
   5.  mdrun - version output 
(https://drive.google.com/open?id=1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6D )

Kind regards,
Chris.


Christopher J. Nelson
High Performance Computing
Direct: +44(0)118 98 55021
F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK

The information in this email and in any attachment(s) is commercial in 
confidence. If you are not the named addressee(s) or if you receive this email 
in error then any distribution, copying or use of this communication or the 
information in it is strictly prohibited. Please notify us immediately by email 
at admin.internet(at)awe.co.uk, and then delete this message from your 
computer. While attachments are virus checked, AWE plc does not accept any 
liability in respect of any virus which is not detected. AWE Plc Registered in 
England and Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR



--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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* Please search the archive at 
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Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

[Paul bauer]

Hello,

if it takes this long then something is going wrong, so you don't need 
to wait that long.

What happens when you build without MPI?

Cheers

Paul

On 20/05/2019 18:14, Nelson Chris AWE wrote:

Thanks Paul,
I have run the binary manually, and it's been going for over an hour now so I 
guess there is something wrong with it - I'll leave it running overnight and 
see if it completes.
Cheers,
Chris

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Paul bauer
Sent: 20 May 2019 15:34
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: EXTERNAL: Re: [gmx-users] gromacs make check failure

Hello,

from looking at the output from make check it looks like this is harmless. The 
tests simply took longer than the internally set cut-off of 30 seconds.
If you are unsure about the build, you can run the test binary manually from 
the build directory with (./gmxpreprocess-test in the same directory where you 
can find the gmx binary).
Then it won't use the cut-off and will take as much time as it will need.

Cheers

Paul

On 20/05/2019 16:26, Nelson Chris AWE wrote:

Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and
OpenMPI

When I run make check, I get a failure on test 29:

29 - GmxPreprocessTests (Timeout)

Any advice would be much appreciated.

Links to output files:

1.  Build environment 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ksdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=vq67KLEfO8%2FOvDEx80mS22FpO4B4WogQbKHS5UKEO%2Bk%3Dreserved=0
 )
2.  Build output 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1PQFllv49M-Op6HLtdKsRJfwHbFeEsintdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=kvDO4%2FnuLOUAz2SemHqGQ2XuN%2Fdzbwz%2B9S4bk%2BAFsfs%3Dreserved=0
 )
3.  Dependency list 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7Tdata=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=ckVLYxFG0XpM797geks%2Fpmd75B5SSDt8EZt8J0Aro5w%3Dreserved=0
 )
4.  Make checkout output 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1data=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9%7C72654b74be024361a62716b132e3fdd0%7C0sdata=ylFHabQdXHeSBIQ4TNhujWeRin5jTkKFv7VAhuCmzR8%3Dreserved=0
 )
5.  mdrun - version output
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdri
ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6Ddata
=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f9
%7C72654b74be024361a62716b132e3fdd0%7C0sdata=UIVAn%2BTTdZx6ljvGQl
%2FQA4jJM1A%2Bbz3dvK8YmGAoBd8%3Dreserved=0 )

Kind regards,
Chris.


Christopher J. Nelson
High Performance Computing
Direct: +44(0)118 98 55021
F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK

The information in this email and in any attachment(s) is commercial
in confidence. If you are not the named addressee(s) or if you receive
this email in error then any distribution, copying or use of this
communication or the information in it is strictly prohibited. Please
notify us immediately by email at admin.internet(at)awe.co.uk, and
then delete this message from your computer. While attachments are
virus checked, AWE plc does not accept any liability in respect of any
virus which is not detected. AWE Plc Registered in England and Wales
Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR


--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

[Paul bauer]

Hello Chris,

in this case I think everything is fine with your build. As you can see 
from the MPI build log it is only the test harness complaining and 
nothing more.

Happy simulations!

Cheers

Paul

On 21/05/2019 16:00, Nelson Chris AWE wrote:

Hi Paul,
If I build without MPI, all tests complete successfully.
Cheers,
Chris.

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Paul bauer
Sent: 20 May 2019 17:27
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] EXTERNAL: Re: gromacs make check failure

Hello,

if it takes this long then something is going wrong, so you don't need to wait 
that long.
What happens when you build without MPI?

Cheers

Paul

On 20/05/2019 18:14, Nelson Chris AWE wrote:

Thanks Paul,
I have run the binary manually, and it's been going for over an hour now so I 
guess there is something wrong with it - I'll leave it running overnight and 
see if it completes.
Cheers,
Chris

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
 On Behalf Of Paul
bauer
Sent: 20 May 2019 15:34
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: EXTERNAL: Re: [gmx-users] gromacs make check failure

Hello,

from looking at the output from make check it looks like this is harmless. The 
tests simply took longer than the internally set cut-off of 30 seconds.
If you are unsure about the build, you can run the test binary manually from 
the build directory with (./gmxpreprocess-test in the same directory where you 
can find the gmx binary).
Then it won't use the cut-off and will take as much time as it will need.

Cheers

Paul

On 20/05/2019 16:26, Nelson Chris AWE wrote:

Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and
OpenMPI

When I run make check, I get a failure on test 29:

29 - GmxPreprocessTests (Timeout)

Any advice would be much appreciated.

Links to output files:

 1.  Build environment 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1tBs6scDqR_gJLtBRzpxMSEdbWwxYR5ksdata=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0sdata=XRtHd3%2FNwAlX04vziL9aQnBvX2xF8v0m%2Fn3vXeG4yFg%3Dreserved=0
 )
 2.  Build output 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1PQFllv49M-Op6HLtdKsRJfwHbFeEsintdata=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0sdata=Ypjb%2BqqeKwSZKMr7NfYJppG8j1xIkf%2BPv%2Fp06RjY9KQ%3Dreserved=0
 )
 3.  Dependency list 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D13rETIX_ejMs1DPBGcTdsQfWKeYFNwd7Tdata=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0sdata=1SvraolwP90kbFWYwmX1k0nTHjgoBg7cx9NBosnZ43M%3Dreserved=0
 )
 4.  Make checkout output 
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1YpAEbPSj0eEe2JERbL6OIc49Gd5e57a1data=01%7C01%7Cchris.nelson%40awe.co.uk%7Cc281092a0d434d6a1ca408d6dd400260%7C72654b74be024361a62716b132e3fdd0%7C0sdata=hIUzlrZ4cVMTCVwCOWUul4HJ7lNpH8v9EspptFO47C8%3Dreserved=0
 )
 5.  mdrun - version output
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdr
i
ve.google.com%2Fopen%3Fid%3D1qu44Mk_aLz3d65YldDKo5mMtvJVyvb6Ddat
a
=01%7C01%7Cchris.nelson%40awe.co.uk%7C9a71d76a0c6d46f4a2e008d6dd3040f
9
%7C72654b74be024361a62716b132e3fdd0%7C0sdata=UIVAn%2BTTdZx6ljvGQ
l
%2FQA4jJM1A%2Bbz3dvK8YmGAoBd8%3Dreserved=0 )

Kind regards,
Chris.


Christopher J. Nelson
High Performance Computing
Direct: +44(0)118 98 55021
F161.1, AWE, Aldermaston, Reading, RG7 4PR, UK

The information in this email and in any attachment(s) is commercial
in confidence. If you are not the named addressee(s) or if you
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Please notify us immediately by email at admin.internet(at)awe.co.uk,
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are virus checked, AWE plc does not accept any liability in respect
of any virus which is not detected. AWE Plc Registered in England and
Wales Registration No 02763902 AWE, Aldermaston, Reading, RG7 4PR

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Re: [gmx-users] About 2019 GMX manual

[Paul bauer]

Hello,

as Benson said, please open an issue at redmine.gromacs.org for all 
kinds of bugs that you find :) (even documentation issues like this)!
After this, you can upload a fix for the issue yourself at 
gerrit.gromacs.org after creating an account there, or one of us will 
get around to do this.


Cheers

Paul

On 07/07/2019 19:59, Benson Muite wrote:

Hi Alan,

This requires making a small change in the git repository at 
https://gerrit.gromacs.org


The relevant line is also mirrored at:

https://github.com/gromacs/gromacs/blob/master/docs/user-guide/system-preparation.rst 



but changes typically go through the git repository at 
gerrit.gromacs.org as indicated at:


http://manual.gromacs.org/documentation/current/dev-manual/overview.html#documentation-organization 



Can make the change on your behalf if it would be helpful.

Benson

On 7/7/19 8:35 PM, Alan wrote:


Is there a better way to report issues with the current manual?

It's a very minor one, to update a link about ACPYPE on page 25.

To use: https://github.com/alanwilter/acpype

Thanks,

Alan



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[gmx-users] GROMACS 2019.4 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.4 is available!

The fourth patch release fixes several issues found since the previous 
patch release of GROMACS 2019.

We encourage all users of the 2019 series to update to 2019.4.
Please see the link to the release notes below for more details.

You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.4.tar.gz
Documentation: http://manual.gromacs.org/2019.4/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.4.tar.gz

Happy simulating!

Paul

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Re: [gmx-users] How to set more mpi for the REMD run?

[Paul bauer]

Hello,

yes, this is indeed possible (see 
http://manual.gromacs.org/current/user-guide/mdrun-features.html#running-multi-simulations 
for more information on multi simulations with GROMACS).
It is just the case that the tutorial system is too small to be 
correctly distributed with domain decomposition. If you use a larger 
system that will work.


Cheers

Paul

On 11/11/2019 14:57, ZHANG Cheng wrote:

Thank you Paul! I want to use more than one mpi processes for each of the REMD, 
would it be possible?




--Original--
From:"ZHANG Cheng"<272699...@qq.com;
Date:Mon, Nov 11, 2019 09:39 PM
To:"gromacs.org_gmx-users"http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B


For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run 
successfully:
gerun mdrun_mpi -v -multidir ./equil[0123]


However, when "#$ -pe mpi 12" is used with the same command, the error message 
told me as the below. Can I ask how to properly set more mpi?




Program:  mdrun_mpi, version 2019.3
Source file: src/gromacs/domdec/domdec.cpp (line 2403)
MPI rank:  6 (out of 12)


Fatal error:
There is no domain decomposition for 3 ranks that is compatible with the given
box and a minimum cell size of 0.8875 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6



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Re: [gmx-users] How to set more mpi for the REMD run?

[Paul bauer]

Hello,

you have set the -mpi option correctly (I think), but the small test 
system used for the tutorial can not be split up over more domains (as 
the  error message tells you).
The idea of the tutorial are here to run on system for each mpi process. 
Are you trying to do the same (and run 12 different simulations), or do 
you want to use several mpi processes for each of the REMD simulations?


Cheers

Paul

On 11/11/2019 14:39, ZHANG Cheng wrote:

I am using the same files based onMark Abraham's REMD tutorial, except 
using a recent Gromacs version 
(gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B


For Stage 1 of the tutorial,when "#$ -pe mpi 4" is used, it can be run 
successfully:
gerun mdrun_mpi -v -multidir ./equil[0123]


However, when "#$ -pe mpi 12" is used with the same command, the error message told 
me as the below. Can I ask how to properly set more mpi?




Program:  mdrun_mpi, version 2019.3
Source file: src/gromacs/domdec/domdec.cpp (line 2403)
MPI rank:  6 (out of 12)


Fatal error:
There is no domain decomposition for 3 ranks that is compatible with the given
box and a minimum cell size of 0.8875 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6



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[gmx-users] Webinar on mdp file settings

[Paul bauer]

Hello @ all GROMACS users,

on December 5th 2019, Christian from core developer team in Stockholm 
will give a webinar explaining the different options available in mdp 
files, and showing how they influence your simulations.


You can find more information about the event here: 
https://bioexcel.eu/webinar-a-walk-through-simulation-parameter-options-mdp-files-for-gromacs-2019-12-05/


or sign up for it here: 
https://attendee.gotowebinar.com/register/5648316978867324429


Hope this will be useful for the community!

Cheers

Paul

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Re: [gmx-users] mac OS Catalina segmentation fault

[Paul bauer]

Hello,

could you try running first with an unmodified version of GROMACS, so we 
can check if the PLUMED modifications are responsible for the crashes 
(unlikely for the tools, but we need to make sure)?
If the vanilla versions are still crashing, can you supply us with some 
log files and input files/run scripts for the failures and open a new 
issue on redmine.gromacs.org?


Also, can you share the full CMakeConfig file?

Cheers

Paul

On 05/11/2019 21:10, Daskalakis Vangelis wrote:

Dear all,
I am running Mac OS Catalina 10.15.1 (Xcode 11.2 11B52). I have
successfully compiled several versions of Gromacs (5.1.5, 2018.8, or
2019.4) patched with plumed (v.2.4.6 for 5.1.5, or v.2.5.3 for 2018/2019
versions). The compilations are completed without any errors, employing the
configuration:
# cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=on
-DCMAKE_INSTALL_PREFIX:PATH=/usr/local/gromacs -DCXX="$MPICXX"

For example Gromacs v. 5.1.5 (but the same is happening on the other
versions), I get segmentation faults, when I just run some tools, like:

[MacBook-Pro:33466] *** Process received signal ***
[MacBook-Pro:33466] Signal: Segmentation fault: 11 (11)
[MacBook-Pro:33466] Signal code:  (0)
[MacBook-Pro:33466] Failing at address: 0x0
[MacBook-Pro:33466] [ 0] 0   libsystem_platform.dylib
  0x7fff69e47b1d _sigtramp + 29
[MacBook-Pro:33466] [ 1] 0   libdyld.dylib
0x7fff69c3730e dyld_stub_binder + 282
[MacBook-Pro:33466] [ 2] 0   libgromacs_mpi.1.5.0.dylib
  0x00010dd60f2e _ZN3gmx24CommandLineModuleManager3runEiPPc + 798
[MacBook-Pro:33466] [ 3] 0   gmx_mpi
0x00010dcc39d1 main + 129
[MacBook-Pro:33466] [ 4] 0   libdyld.dylib
0x7fff69c462e5 start + 1
[MacBook-Pro:33466] [ 5] 0   ???
0x0002 0x0 + 2
[MacBook-Pro:33466] *** End of error message ***
zsh: segmentation fault  gmx_mpi trjconv

switching MPI support on/ off on the configuration/ compilation stage does
not change the situation. Some tools are running smoothly, as editconf.
However others, have segmentation faults. Grompp is running on v.5.1.5, but
gives a segmantation fault on v. 2019.4.

I would appreciate some help,
thank you,
Vangelis.



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Re: [gmx-users] Error in DNA.itp file

[Paul bauer]

Hello,

the error states that you are missing parameters for your system. Did 
you check that the forcefield contains all the special parameters you 
need for the conjugate molecule?
Also, I would recommend to not use a prehistoric version of GROMACS for 
new studies, if there are no specific reasons preventing you from using 
a more recent one that is still supported (such as 2018 or 2019).


Cheers

Paul

On 05/11/2019 14:47, Ayesha Kanwal wrote:

Hi all,
i am preparing system of DNA-protein complex, downloaded it from RCSB website, 
by using GROMACS-version 4.5.5; force field AMBER03WS with water Model TIP4P 
(2005). The DNA chain contains DA, DT, DG, DC atom type.
but the problem is that when i use command for energy minimization the 
following error has occurred. Error shows that problem is in .itp file Dih. 
types. For protein .itp files,there was no problem. Only DNA .itp files have 
issue. Its my first time i am preparing this kind of system please let me know 
how can i resolve this problem and why these errors were generated ? I have 
searched out previous mail but could not find relevant answer so i am posting 
it now here. i have attached .mdp file with this e-mail.

checking input for internal consistency...
Generated 2412 of the 2415 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2415 of the 2415 1-4 parameter combinations

ERROR 1 [file dna-his_DNA_chain_I.itp, line 44148]:
   No default Improper Dih. types


ERROR 2 [file dna-his_DNA_chain_J.itp, line 44148]:
   No default Improper Dih. types




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[gmx-users] Third beta release of GROMACS 2020

[Paul bauer]

Hi GROMACS users,

The third and final beta release of GROMACS 2020 is now out and available!

As before, we are making the testing versions available for you to be 
able to get feedback
on how well things are working, and what could be improved or if there 
are any bugs

in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, 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.)
* Running all parts of a simulation on the GPU by offloading the update 
and constraint calculations

* Fitting structures into experimental density maps
* The improved Python API

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2019.4
and patches for the upcoming 2019.5 version are present, apart from 
features that have been removed.


If all goes to plan, we hope to ship the final 2020 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.

The release candidate will be available in mid-December, before the 
final release.


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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta3.tar.gz
Documentation: http://manual.gromacs.org/documentation/2020-beta3/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2020-beta3/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2020-beta3.tar.gz

Happy testing!

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Re: [gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

[Paul bauer]

Hello,

the error you are getting in the end means that your simulation likely 
does not use PME, or uses it in a way that is not implemented to run on 
the GPU.
You can still run the nonbonded calculations on the GPU, just remove the 
-pme gpu flag.


For running different simulations on your GPUs, you need to set the 
environment variable CUDA_VISIBLE_DEVICES so that each simulation only 
sees on of the available GPUs.


Cheers

Paul

On 13/12/2019 06:22, Pragati Sharma wrote:

Hello all,

I am running a polymer melt with 10 atoms, 2 fs time step, PME, on a
workstation with specifications:

2X Intel Xeon 6128 3.4 2666 MHz 6-core CPU
2X16B DDR4 RAM
2XRTX 2080Ti 11 GB

I have installed *GPU and thread_mpi *enabled gromacs 2019.0 version using:

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
*-DGMX_THREAD_MPI=ON
-DGMX_GPU=ON*

While running a single job with below command, I am getting a performance
of *65 ns/day. *

*gmx_tmpi mdrun -v -s t1.tpr -c t1.pdb -gpu_id 0 -ntmpi 1 -ntomp 24*

*Q. However I want to run two different simulations at a time using CPU
cores and one GPU for each, Can somebody help me with mdrun command (what
combination of ntmpi and ntomp) I should use to run two simulations with
efficient utilization of CPU cores and 1 GPU each.*

*Q.* I have also tried utilising GPU for PME calculations using -pme GPU,
as in the command

gmx_tmpi mdrun -v -s t1.tpr -c t1.pdb -ntmpi 1 -ntomp 24  -gputasks 01* -nb
gpu -pme gpu*

but i get the below error,


*"Feature not implemented:The input simulation did not use PME in a way
that is supported on the GPU."*

why is this error coming? Should I put extra attributes while compiling
gromacs.

Thanks



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Re: [gmx-users] Signal: Floating point exception (8) Signal code: Floating point divide-by-zero (3)

[Paul bauer]

Hello,

I'll have a look later today.
Can you also give as information about your build configuration?
If you could upload a log file from mdrun to Redmine it should be enough.

Thanks

Paul

On 12/12/2019 11:28, Dave M wrote:

Hi Mark,

Thanks just opened new issue. My all simulations are performed using
gromacs2019.4 and to be consistent to report the results I would like to
keep same version. But this specific case is creating trouble. What is best
I can do? if I use a different gromacs version for this specific case then
it would look bit unusual from reviewer's point of view.

Dave

On Thu, Dec 12, 2019 at 1:20 AM Mark Abraham 
wrote:


Hi,

That sounds very much like a bug, but it's hard to say where it comes from.
Can you please open an issue at https://redmine.gromacs.org/ and attach
your .tpr files plus a log file from a failing run and the above stack
trace?

Mark

On Thu, 12 Dec 2019 at 08:37, Dave M  wrote:


Hi All,

I am getting errors which I don't understand. I ran a simulation (gromacs
2019.4) which completed fine. Then, with exactly the same system and mdp
files, I ran three repeats with different velocity seeds (so initial
configuration is same) but each simulation ended incomplete at different
time steps. My system does not blow or anything like that. Every time am
getting this error for the repeats with different velocity seeds. Also,

if

I use cpt file to restart the job it ends at the same time step where it
got killed earlier.
My command line is:
gmx_mpi mdrun -deffnm 04-run -rdd 2.0

*** Process received signal ***

  Signal: Floating point exception (8)

  Signal code: Floating point divide-by-zero (3)

  Failing at address: 0x7ff112f22075

  [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef20)[0x7ff11c40cf20]

  [ 1] /lib/x86_64-linux-gnu/libm.so.6(+0x86075)[0x7ff112f22075]

  [ 2]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZSt3logf+0x1d)[0x7ff11d576c10]

  [ 3]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx17GammaDistributionIfEclINS_12ThreeFry2x64ILj64EfRT_RKNS1_10param_typeE+0x21f)[0x7ff11e1302bf]

  [ 4]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx17GammaDistributionIfEclINS_12ThreeFry2x64ILj64EfRT_+0x27)[0x7ff11e12fdd7]

  [ 5]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(+0x13cecd1)[0x7ff11e12ecd1]

  [ 6]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(+0x13cee10)[0x7ff11e12ee10]

  [ 7]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_Z15vrescale_tcouplPK10t_inputreclP14gmx_ekindata_tfPd+0x1de)[0x7ff11e12f0a6]

  [ 8]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_Z14update_tcouplelPK10t_inputrecP7t_stateP14gmx_ekindata_tPK9t_extmassPK9t_mdatoms+0x1b3)[0x7ff11e1d6339]

  [ 9]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx10Integrator5do_mdEv+0x43eb)[0x7ff11e286d45]

  [10]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx10Integrator3runEjb+0x1a7)[0x7ff11e280a1b]

  [11]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx8Mdrunner8mdrunnerEv+0x3a69)[0x7ff11e2a79e5]

  [12] gmx_mpi(+0xe37c)[0x55a41da7937c]

  [13]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(+0x64e29f)[0x7ff11d3ae29f]

  [14]



/usr/local/gromacs/gromacs2019_4/lib/libgromacs_mpi.so.4(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x3d6)[0x7ff11d3aff16]

  [15] gmx_mpi(+0xbaa1)[0x55a41da76aa1]

  [16]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7ff11c3efb97]

  [17] gmx_mpi(+0xb91a)[0x55a41da7691a]

Any idea what could be wrong? Suggestions much appreciated.

Thanks.

Dave
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Re: [gmx-users] Fwd: gmx trjcat

[Paul bauer]

Hello,

this looks like a case of misleading documentation. Can you file an 
issue for this please on redmine.gromacs.org?

So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your files 
to e.g. XTC format, use trjcat to combine them and convert them back to GRO.


Cheers

Paul


On 27/10/2019 19:47, Alex wrote:

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files, according the
gmx trjcat man page;

Options to specify input files:
  -f  [<.xtc/.trr/...> [...]] (traj.xtc)
Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex



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0046737308594

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Re: [gmx-users] Fwd: gmx trjcat

[Paul bauer]

Hello,

I think I understood your problem (or at least hope so).
The issue is that it is no longer possible to directly concatenate text 
based trajectory files, so I showed a possible way to work around the 
problem.
You can also go back to a previous version of GROMACS to perform the 
concatenation, but I can't promise you that it will work.


Please let me know if you need extra help to get this to work.

@Justin, here is the change that added the check for binary file 
formats: c232242c29fb3ca63c8e1027eb70477069decdd9


Cheers

Paul

On 28/10/2019 15:42, Alex wrote:

Hi,
Paul,
I guess you understood the question wrongly. I have some *.gro files and I
want to concatenate them to have a trr (or xtc) trajectory.

Justin,
Yes indeed, It would be great if gmx trjcat could concatenate the gro files.

Regards,
Alex

On Mon, Oct 28, 2019 at 9:03 AM Justin Lemkul  wrote:



On 10/28/19 6:26 AM, Paul bauer wrote:

Hello,

this looks like a case of misleading documentation. Can you file an
issue for this please on redmine.gromacs.org?
So that we don't forgot to fix this for the next patch release?
A possible work around for you can be that you first convert your
files to e.g. XTC format, use trjcat to combine them and convert them
back to GRO.


Out of curiosity, why was this file format removed as an input for
trjcat? Was it a conscious choice? The ability to concatenate e.g. PDB
files to make a psuedo-trajectory for ensemble analysis was rather
handy. Converting to an intermediate binary format is a workaround, but
why add the extra step? Did the trjcat code need de-complicating?

-Justin


Cheers

Paul


On 27/10/2019 19:47, Alex wrote:

Any comment on this, please?
Thanks
-- Forwarded message -
From: Alex 
Date: Sat, Oct 26, 2019 at 9:38 AM
Subject: gmx trjcat
To: 


Dear all,
I want to concatenate some gro file to have a trr or xtc trajectory file
out of them as gro files are also acceptable as input files,
according the
gmx trjcat man page;

Options to specify input files:
   -f  [<.xtc/.trr/...> [...]] (traj.xtc)
 Trajectory: xtc trr cpt *gro* g96 pdb tng

So, I fed the .gro files in as input files likes;
gmx trjcat -f c*.gro -o trajout.trr

However, I get below error that;
Fatal error:
gmx trjcat can only handle binary trajectory formats (trr, xtc, tng)

Any comment is highly appreciated.
Regards,
Alex



--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] regression test errors

[Paul bauer]

Hello Dave,

I thought it was something like that.
The error is harmless (just telling you that MPI is doing its job), and 
the testing script gets confused because of the extra message in the 
output file.


So I think you are good to go (and we need to do something about the 
testing script).


Happy simulating!

Cheers

Paul

On 23/10/2019 13:39, Dave M wrote:

Hi Paul,

I checked using this command for a specific folder, and I used '-mpirun
mdrun' rather '-mpirun mpirun':


./gmxtest.pl -mpirun mdrun -np 2 -noverbose rotation



I get lot of these errors:


topol.tpr file different from ./reference_s.tpr. Check files in flex for
flex

FAILED. Check checktpr.out, checktpr.err file(s) in flex for flex

topol.tpr file different from ./reference_s.tpr. Check files in flex-t for
flex-t

FAILED. Check checktpr.out, checktpr.err file(s) in flex-t for flex-t

topol.tpr file different from ./reference_s.tpr. Check files in flex2 for
flex2

FAILED. Check checktpr.out, checktpr.err file(s) in flex2 for flex2

topol.tpr file different from ./reference_s.tpr. Check files in flex2-t for
flex2-t

FAILED. Check checktpr.out, checktpr.err file(s) in flex2-t for flex2-t


 so on



A)  the only suspicious thing I see in checktpr.err is possibly different
software versions.


Command line:

   gmx_mpi check -s1 ./reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol
0.001


Note: When comparing run input files, default tolerances are reduced.

Reading file ./reference_s.tpr, VERSION 5.0-beta2-dev-20140130-02adca5
(single precision)

Note: file tpx version 96, software tpx version 116

Reading file topol.tpr, VERSION 2019.4 (single precision)




B) And Only suspicious thing I see in checktpr.out is pasted below (I have
removed the host ip number). Just to mention I use Amazon web services so
probably the following error is related to instance when it was created and
then stored as an image and then re-used with a different ip. May be am
just talking silly!


[[2115,1],0]: A high-performance Open MPI point-to-point messaging module

was unable to find any relevant network interfaces:


Module: OpenFabrics (openib)

   Host: ip-xxx-xx-xx-xxx


Another transport will be used instead, although this may result in

lower performance.


NOTE: You can disable this warning by setting the MCA parameter

btl_base_warn_component_unused to 0.


On Wed, Oct 23, 2019 at 4:10 AM Paul bauer  wrote:


Hello Dave,

this is weird, no idea why it didn't work then.
You can try running the test suite manually in the folder you found with

perl gmxtest.pl -mpirun mpirun -np X -noverbose

That will show if the test binary works and should report any failing
tests.
Don't forget to source the GMXRC file before trying, though!

Cheers

Paul


On 23/10/2019 12:36, Dave M wrote:

Hi Paul,

Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now.

Regarding tests, I found the folder here build/tests/regressiontests
So I checked all the log using a simple script (searching keyword
'Finished') and it shows that all the log files have Finished properly

in

their corresponding folders. So log files do not say anything here.

On Wed, Oct 23, 2019 at 3:07 AM Paul Bauer 

wrote:

Hello Dave,

You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a

MPI

enabled build of GROMACS. This is what the error message tries to tell

you,

but we might need to improve on this.

There should be a regressiontests folder somewhere in your build tree

if it

downloaded the tests correctly.

Cheers

Paul

On Wed, 23 Oct 2019, 12:02 Dave M,  wrote:


Hi Paul,

Thanks for your reply.
a) I just checked there is no tests/regressiontests, some other folder

is

there test/sphysicalvalidation
There is no log file.
b) Regarding thread-mpi I think it is not installed because when I use

some

command like this:


gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2

I get an error:


Fatal error:

Setting the total number of threads is only supported with thread-MPI

and

GROMACS was compiled without thread-MPI

I think (please correct me) gmx_mpi is for external MPI  openMPI in my

case

so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command not
found. I am not sure what I missed in installation cmake flags.

Dave

On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer 

wrote:

Hello Dave,

Did you have a look into the log files from the regression tests under
tests/regressiontests?
They might give us some insight into what is happening.

The warning in respect to thread-MPI is harmless, it just tells you

that

you are using real MPI instead of thread-MPI.

Cheers
Paul

On Wed, 23 Oct 2019, 07:36 Dave M,  wrote:


Hi All,

Any hints/help much appreciated why am getting regression tests

failure.

Also to mention I think thread-mpi was not installed as I got an

error

saying "MPI is not compatible with thread-MPI. Disabling thread-MPI".

How

to check the compatibility?

Thanks.

best regards,
D

On Sun, Oct 20, 2019 at 2:58 AM Dave M 

wrote:

Hi All,

I

Re: [gmx-users] regression test errors

[Paul Bauer]

Hello Dave,

You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a MPI
enabled build of GROMACS. This is what the error message tries to tell you,
but we might need to improve on this.

There should be a regressiontests folder somewhere in your build tree if it
downloaded the tests correctly.

Cheers

Paul

On Wed, 23 Oct 2019, 12:02 Dave M,  wrote:

> Hi Paul,
>
> Thanks for your reply.
> a) I just checked there is no tests/regressiontests, some other folder is
> there test/sphysicalvalidation
> There is no log file.
> b) Regarding thread-mpi I think it is not installed because when I use some
> command like this:
>
>
> gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2
>
> I get an error:
>
>
> Fatal error:
>
> Setting the total number of threads is only supported with thread-MPI and
> GROMACS was compiled without thread-MPI
>
> I think (please correct me) gmx_mpi is for external MPI  openMPI in my case
> so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command not
> found. I am not sure what I missed in installation cmake flags.
>
> Dave
>
> On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer  wrote:
>
> > Hello Dave,
> >
> > Did you have a look into the log files from the regression tests under
> > tests/regressiontests?
> > They might give us some insight into what is happening.
> >
> > The warning in respect to thread-MPI is harmless, it just tells you that
> > you are using real MPI instead of thread-MPI.
> >
> > Cheers
> > Paul
> >
> > On Wed, 23 Oct 2019, 07:36 Dave M,  wrote:
> >
> > > Hi All,
> > >
> > > Any hints/help much appreciated why am getting regression tests
> failure.
> > > Also to mention I think thread-mpi was not installed as I got an error
> > > saying "MPI is not compatible with thread-MPI. Disabling thread-MPI".
> How
> > > to check the compatibility?
> > >
> > > Thanks.
> > >
> > > best regards,
> > > D
> > >
> > > On Sun, Oct 20, 2019 at 2:58 AM Dave M  wrote:
> > >
> > > > Hi All,
> > > >
> > > > I am trying to install gromacs2019.4 with:
> > > > cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
> > > > -DGMX_MPI=on -DGMX_GPU=on
> > > > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
> > > > -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug
> > > >
> > > > But 5 tests (41 to 46) were failed copied below:
> > > >
> > > >
> > > > The following tests FAILED:
> > > >
> > > > 41 - regressiontests/simple (Failed)
> > > >
> > > > 42 - regressiontests/complex (Failed)
> > > >
> > > > 43 - regressiontests/kernel (Failed)
> > > >
> > > > 44 - regressiontests/freeenergy (Failed)
> > > >
> > > > 45 - regressiontests/rotation (Failed)
> > > >
> > > > Errors while running CTest
> > > >
> > > > CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> > > > 'CMakeFiles/run-ctest-nophys' failed
> > > >
> > > > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> > > >
> > > > CMakeFiles/Makefile2:1392: recipe for target
> > > > 'CMakeFiles/run-ctest-nophys.dir/all' failed
> > > >
> > > > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> > > >
> > > > CMakeFiles/Makefile2:1172: recipe for target
> > 'CMakeFiles/check.dir/rule'
> > > > failed
> > > >
> > > > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > > >
> > > > Makefile:626: recipe for target 'check' failed
> > > > make: *** [check] Error 2
> > > >
> > > > Not sure what could be wrong. Just to add I get some error/warning
> > during
> > > > installation which says "MPI is not compatible with thread-MPI.
> > Disabling
> > > > thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu
> > 18.04
> > > I
> > > > used "sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev"
> > > >
> > > > Please let me know how I can fix this.
> > > >
> > > > best regards,
> > > > D
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List b

Re: [gmx-users] regression test errors

[Paul bauer]

Hello Dave,

this is weird, no idea why it didn't work then.
You can try running the test suite manually in the folder you found with

perl gmxtest.pl -mpirun mpirun -np X -noverbose

That will show if the test binary works and should report any failing tests.
Don't forget to source the GMXRC file before trying, though!

Cheers

Paul


On 23/10/2019 12:36, Dave M wrote:

Hi Paul,

Thanks for the 'mpirun -n X gmx_mpi mdrun'. It works now.

Regarding tests, I found the folder here build/tests/regressiontests
So I checked all the log using a simple script (searching keyword
'Finished') and it shows that all the log files have Finished properly  in
their corresponding folders. So log files do not say anything here.

On Wed, Oct 23, 2019 at 3:07 AM Paul Bauer  wrote:


Hello Dave,

You need to use mpirun -n (number of processes) gmx_mpi mdrun to use a MPI
enabled build of GROMACS. This is what the error message tries to tell you,
but we might need to improve on this.

There should be a regressiontests folder somewhere in your build tree if it
downloaded the tests correctly.

Cheers

Paul

On Wed, 23 Oct 2019, 12:02 Dave M,  wrote:


Hi Paul,

Thanks for your reply.
a) I just checked there is no tests/regressiontests, some other folder is
there test/sphysicalvalidation
There is no log file.
b) Regarding thread-mpi I think it is not installed because when I use

some

command like this:


gmx_mpi mdrun -v -deffnm 03-run -rdd 2.0 -nt 2

I get an error:


Fatal error:

Setting the total number of threads is only supported with thread-MPI and
GROMACS was compiled without thread-MPI

I think (please correct me) gmx_mpi is for external MPI  openMPI in my

case

so I tried just 'gmx mdrun' (not gmx_mpi) but then it says command not
found. I am not sure what I missed in installation cmake flags.

Dave

On Wed, Oct 23, 2019 at 2:45 AM Paul Bauer 

wrote:

Hello Dave,

Did you have a look into the log files from the regression tests under
tests/regressiontests?
They might give us some insight into what is happening.

The warning in respect to thread-MPI is harmless, it just tells you

that

you are using real MPI instead of thread-MPI.

Cheers
Paul

On Wed, 23 Oct 2019, 07:36 Dave M,  wrote:


Hi All,

Any hints/help much appreciated why am getting regression tests

failure.

Also to mention I think thread-mpi was not installed as I got an

error

saying "MPI is not compatible with thread-MPI. Disabling thread-MPI".

How

to check the compatibility?

Thanks.

best regards,
D

On Sun, Oct 20, 2019 at 2:58 AM Dave M 

wrote:

Hi All,

I am trying to install gromacs2019.4 with:
cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
-DGMX_MPI=on -DGMX_GPU=on
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
-DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug

But 5 tests (41 to 46) were failed copied below:


The following tests FAILED:

41 - regressiontests/simple (Failed)

42 - regressiontests/complex (Failed)

43 - regressiontests/kernel (Failed)

44 - regressiontests/freeenergy (Failed)

45 - regressiontests/rotation (Failed)

Errors while running CTest

CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failed

make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8

CMakeFiles/Makefile2:1392: recipe for target
'CMakeFiles/run-ctest-nophys.dir/all' failed

make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2

CMakeFiles/Makefile2:1172: recipe for target

'CMakeFiles/check.dir/rule'

failed

make[1]: *** [CMakeFiles/check.dir/rule] Error 2

Makefile:626: recipe for target 'check' failed
make: *** [check] Error 2

Not sure what could be wrong. Just to add I get some error/warning

during

installation which says "MPI is not compatible with thread-MPI.

Disabling

thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu

18.04

I

used "sudo apt-get install openmpi-bin openmpi-common

libopenmpi-dev"

Please let me know how I can fix this.

best regards,
D



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Re: [gmx-users] regression test errors

[Paul Bauer]

Hello Dave,

Did you have a look into the log files from the regression tests under
tests/regressiontests?
They might give us some insight into what is happening.

The warning in respect to thread-MPI is harmless, it just tells you that
you are using real MPI instead of thread-MPI.

Cheers
Paul

On Wed, 23 Oct 2019, 07:36 Dave M,  wrote:

> Hi All,
>
> Any hints/help much appreciated why am getting regression tests failure.
> Also to mention I think thread-mpi was not installed as I got an error
> saying "MPI is not compatible with thread-MPI. Disabling thread-MPI". How
> to check the compatibility?
>
> Thanks.
>
> best regards,
> D
>
> On Sun, Oct 20, 2019 at 2:58 AM Dave M  wrote:
>
> > Hi All,
> >
> > I am trying to install gromacs2019.4 with:
> > cmake ..  -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=on
> > -DGMX_MPI=on -DGMX_GPU=on
> > -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs2019_4
> > -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Debug
> >
> > But 5 tests (41 to 46) were failed copied below:
> >
> >
> > The following tests FAILED:
> >
> > 41 - regressiontests/simple (Failed)
> >
> > 42 - regressiontests/complex (Failed)
> >
> > 43 - regressiontests/kernel (Failed)
> >
> > 44 - regressiontests/freeenergy (Failed)
> >
> > 45 - regressiontests/rotation (Failed)
> >
> > Errors while running CTest
> >
> > CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
> > 'CMakeFiles/run-ctest-nophys' failed
> >
> > make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
> >
> > CMakeFiles/Makefile2:1392: recipe for target
> > 'CMakeFiles/run-ctest-nophys.dir/all' failed
> >
> > make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
> >
> > CMakeFiles/Makefile2:1172: recipe for target 'CMakeFiles/check.dir/rule'
> > failed
> >
> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> >
> > Makefile:626: recipe for target 'check' failed
> > make: *** [check] Error 2
> >
> > Not sure what could be wrong. Just to add I get some error/warning during
> > installation which says "MPI is not compatible with thread-MPI. Disabling
> > thread-MPI". I am using -DGMX_MPI=on and to have openMPI on ubuntu 18.04
> I
> > used "sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev"
> >
> > Please let me know how I can fix this.
> >
> > best regards,
> > D
> >
> >
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[gmx-users] Second beta release of GROMACS 2020

[Paul bauer]

Hi GROMACS users,

The second beta release of GROMACS 2020 is now out and available!

As before, we are making the testing versions available for you to be 
able to get feedback
on how well things are working, and what could be improved or if there 
are any bugs

in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, 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.)
* Running all parts of a simulation on the GPU by offloading the update 
and constraint calculations

* Fitting structures into experimental density maps
* The improved Python API

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2019.4
is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2020 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.

There is another beta release planned for the end of November, as well
as at least one release candidate in December.

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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020-beta2.tar.gz
Documentation: http://manual.gromacs.org/documentation/2020-beta2/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2020-beta2/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2020-beta2.tar.gz

Happy testing!

--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] Free webinar on accelerating sampling in GROMACS with the AWH method

[Paul bauer]

Hi,

Since version 2018, GROMACS supports the Accelerated Weight Histogram 
method to accelerate sampling along reaction coordinates. With AWH 
conformational transitions can be accelerated by orders of magnitude.


On Tuesday, September 24, from 15:00 we are organizing a free webinar on 
the AWH method presented by the main developer Berk Hess.
At the end of the webinar we'll have a Q session during which you can 
ask Berk questions directly.


More information about the webinar and how to join is here:
https://bioexcel.eu/webinar-accelerating-sampling-in-gromacs-with-the-awh-method-2019-09-24/

Cheers

Paul

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[gmx-users] First beta release of GROMACS 2020

[Paul bauer]

Hi GROMACS users,

The first beta release of GROMACS 2020 is available!

We are making this available to you to get an early taste of how GROMACS
2020 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!

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.)
* Modular simulator for running a number of default simulations.
* Improved support for gmxapi Python API, version 0.1.0
* Ability to run density guided simulations.

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2019.3
is present, (as well as some fixes targeted at 2019.4),
apart from features that have been removed.

If all goes to plan, we hope to ship the final 2020 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-2020-beta1.tar.gz
Documentation: http://manual.gromacs.org/documentation/2020-beta1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/documentation/2020-beta1/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2020-beta1.tar.gz

Happy testing!

--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] Implicit Solvent and Box Size

[Paul bauer]

Hello,

the implicit solvent functionality has been deprecated a while ago in 
GROMACS and has been removed in the recent versions.


Can the simulations also be run in explicit solvents (that are a better 
physical representation anyway)?


Cheers

Paul

On 07/10/2019 16:50, 张 卓 wrote:

Hi, I am doing the aggregations of small peptides in implicit solvents. 
However, it seems that there is no detailed tutorial on such subject and I just 
turned on the 'implicit solvent' option in the .mdp file. However, I found that 
the box was compressed during mdrun. It comes to me that the implicit solvent 
is only a field rather than some virtual material. I believe that the 
compression should be due to pressure coupling.  Then should I use NPT ensemble 
for implicit solvents. If so, how can I keep the box size with pressure 
coupling?


Thanks for your help!


Regards,

Zhuo



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Re: [gmx-users] Need help with installation of Gromacs-2019.3 with Intell compilers

[Paul bauer]

Hej,

I can't access the repository, so I can't say for certain what happened.
Can you share your cmake command line?

Cheers

Paul

On 07/10/2019 21:25, Lyudmyla Dorosh wrote:

Hello Gromacs Developers/Users,

I'm trying to install Gromacs-2019.3 on Intel Xeon W-2175 with Intel
compilers (+MKL+MPI).
First I compiled cmake with Intel compilers. All output files are attached.
cmake, make seemed to go ok, but all check test failed. What do I do wrong?
https://drive.google.com/file/d/1M8aOaq7ocmK4UOAzcRb5AqWMihIhVtmn/view?usp=sharing

Thank you,

Lyudmyla Dorosh, PhD

University of Alberta
Department of Electrical and Computer Engineering,
4-021 ECERF
Edmonton, AB, T6G 2G8
Canada
Email: dor...@ualberta.ca



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[gmx-users] GROMACS 2018.8 patch release available

[Paul bauer]

Hi GROMACS users,

I just released another patch release of GROMACS 2018, bringing the 
official version to 2018.8!


We decided to release this additional patch due to the one big issue 
that was still present in the 2018 branch that could affect scientific 
correctness, so we encourage all users of the 2018
series to update to 2018.8. Please see the link to the release notes 
below for more details.
The 2018 branch continues to be in support only for issues that affect 
scientific issues, while the 2019 branch is under active support.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.8.tar.gz
Documentation: http://manual.gromacs.org/2018.8/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2018.8.tar.gz

Happy simulating!

Paul

--
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GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] GROMACS 2020 release candidate

[Paul bauer]

Hi GROMACS users,

The GROMACS 2020 release candidate is now out and available!

As before, we are making the testing versions available for you to be 
able to get feedback
on how well things are working, and what could be improved or if there 
are any bugs

in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, please do not use this version for doing science you plan to 
publish -
even though it should be stable now, we still want to use the last weeks 
to iron out

any remaining issues that might show up. 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.)
* Running all parts of a simulation on the GPU by offloading the update 
and constraint calculations

* Fitting structures into experimental density maps
* The improved Python API

There’s lots of other new things, and a few old things removed - please see
the release notes for the complete list. All the content of GROMACS 2019.4
is present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2020 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-2020-rc1.tar.gz
Documentation: http://manual.gromacs.org/2020-rc1/index.html
(includes install guide, user guide, reference manual)
Release Notes:
http://manual.gromacs.org/2020-rc1/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2020-rc1.tar.gz

Happy testing!

--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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[gmx-users] GROMACS 2019.5 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.5 is available!

The fifth patch release fixes several issues found since the previous 
patch release of GROMACS 2019.

We encourage all users of the 2019 series to update to 2019.5.
Please see the link to the release notes below for more details.

Please note that this is the final patch release for 2019 while the 
branch is under full maintenance, with only critical scientific issues 
being fixed from now on.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.5.tar.gz
Documentation: http://manual.gromacs.org/2019.5/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.5.tar.gz

Happy simulating!

Paul

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0046737308594

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Re: [gmx-users] GROMACS 2020 release candidate

[Paul bauer]

Hello,

we have not been able to port everything from the group scheme to verlet 
yet, so some things will be unsupported in 2020.
For those things I would advice people to stick to 2019 for the time 
being, while we are working on porting the remaining things over for the 
2021 release next year.


Cheers

Paul

On 23/12/2019 12:47, Tafelmeier, Stefanie wrote:

Dear Paul,

I just installed the Gomacs 2020 rc1 for testing and would like to give some 
feedback.

As we are working partly with the flexible Williams force field, it is 
nessecary to use Buckingham potential.
Until now this was only possible when using group cutoff scheme.

I was excited to here, that it will be gone - as it takes ages - with the new 
gromacs verions and verlet should support all.
But when trying it, it says:

---
Program: gmx mdrun, version 2020-rc1
Source file: src/gromacs/mdlib/forcerec.cpp (line 1313)

Fatal error:
Verlet cutoff-scheme is not supported with Buckingham

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

But group cannot be used anymore.

Is there any other way to use Buckingham now?

Many thanks for your answer in advance.
Best wishes,
Steffi





-Ursprüngliche Nachricht-
Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 Im Auftrag von Paul bauer
Gesendet: Freitag, 20. Dezember 2019 15:54
An: gromacs.org_gmx-users@maillist.sys.kth.se; gmx-annou...@gromacs.org
Betreff: [gmx-users] GROMACS 2020 release candidate

Hi GROMACS users,

The GROMACS 2020 release candidate is now out and available!

As before, we are making the testing versions available for you to be able to 
get feedback on how well things are working, and what could be improved or if 
there are any bugs in the code we have missed ourselves.

We really appreciate your testing of the new release with 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!

As before, please do not use this version for doing science you plan to publish 
- even though it should be stable now, we still want to use the last weeks to 
iron out any remaining issues that might show up. 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.)
* Running all parts of a simulation on the GPU by offloading the update and 
constraint calculations
* Fitting structures into experimental density maps
* The improved Python API

There’s lots of other new things, and a few old things removed - please see the 
release notes for the complete list. All the content of GROMACS 2019.4 is 
present, apart from features that have been removed.

If all goes to plan, we hope to ship the final 2020 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-2020-rc1.tar.gz
Documentation: http://manual.gromacs.org/2020-rc1/index.html
(includes install guide, user guide, reference manual) Release Notes:
http://manual.gromacs.org/2020-rc1/release-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2020-rc1.tar.gz

Happy testing!

--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594

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0046737308594

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Re: [gmx-users] Call for Abstracts: SES - Advances in Polymer Modeling and Simulations (deadline March 17, 2020)

[Paul bauer]

Hello,

please do ***NOT*** use the mailing list for those kinds of 
announcements in the future.
It is supposed to be for people discussing and asking for help with 
GROMACS, not for advertising conferences.


Thanks

Paul

On 12/02/2020 19:13, Jihong Ma wrote:

Dear colleagues,

The Society of Engineering Science (SES) 57th Annual Technical Meeting will
be held at Hyatt Regency Minneapolis, September 28-30, 2020 (
https://ccaps.umn.edu/SES).

As part of this meeting, we are organizing a mini-symposium addressing
the *advances
in polymer modeling and simulations* under Track 7 - Soft, Active Materials
and Applications in Soft Robotics.

The production of newer classes of polymers, such as polymerized ionic
liquids and nanoporous polymers, opened up exciting possibilities for
various applications including electrochemical energy generation and
storage, water purification, sensing and releasing biological molecules,
development of light-weight structures. Modeling these complex
architectures presents significant challenges related, for instance, to the
system size, accuracy of the classical and coarse-grained potentials,
presence of multi-scale effects, and critical discrepancies with experiment.

This mini-symposium aims to bring together scientists and engineers working
at the forefront of the modeling and simulation to exchange and share their
experiences and recent research results.

We cordially invite all the interested scholars to submit your abstract to
this mini-symposium. The deadline for submission is *March 17, 2020*.

We look forward to your presentations at our symposium.



Best regards,

Jihong Ma, University of Vermont

Traian Dumitrica, University of Minnesota - Twin Cities



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Re: [gmx-users] Performance issues with Gromacs 2020 on GPUs - slower than 2019.5

[Paul bauer]

Hello,

you can't add attachments to the list, please upload the files somewhere 
to share them.
This might be quite important to us, because the performance regression 
is not expected by us.


Cheers

Paul

On 26/02/2020 15:54, Andreas Baer wrote:

Hello,

from a set of benchmark tests with large systems using Gromacs 
versions 2019.5 and 2020, I obtained some unexpected results:
With the same set of parameters and the 2020 version, I obtain a 
performance that is about 2/3 of the 2019.5 version. Interestingly, 
according to nvidia-smi, the GPU usage is about 20% higher for the 
2020 version.
Also from the log files it seems, that the 2020 version does the 
computations more efficiently, but spends so much more time waiting, 
that the overall performance drops.


Some background info on the benchmarks:
- System contains about 2.1 million atoms.
- Hardware: 2x Intel Xeon Gold 6134 („Skylake“) @3.2 GHz = 16 cores + 
SMT; 4x NVIDIA Tesla V100
  (similar results with less significant performance drop (~15%) on a 
different machine: 2 or 4 nodes with each [2x Intel Xeon 2660v2 („Ivy 
Bridge“) @ 2.2GHz = 20 cores + SMT; 2x NVIDIA Kepler K20])
- Several options for -ntmpi, -ntomp, -bonded, -pme are used to find 
the optimal set. However the performance drop seems to be persistent 
for all such options.


Two representative log files are attached.
Does anyone have an idea, where this drop comes from, and how to 
choose the parameters for the 2020 version to circumvent this?


Regards,
Andreas



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Re: [gmx-users] install and mdrun problems

[Paul bauer]

Hello,

If you try an updated version, please try an actually recent one, either 
2019.6 or the 2020 release.
If you could provide us with some error or log messages we might be able 
to find out what happened there.


Cheers

Paul

On 02/03/2020 16:03, Kamran Gul, M.Phil. Scholar, Institute of Chemical 
Sciences, UoP wrote:

Try gromacs 2019.2.
And then update your cuda and nvidia.

On Mon, 2 Mar 2020, 6:58 p.m. Kunal Dutta,  wrote:


Hello Sir,
May I know the detailed configuration of your system.
Sincerely,
Kunal




On Mon, 2 Mar 2020 at 09:08, Bogdanov, Vladimir 
wrote:


Hi all,

I installed Gromacs2020 on ubuntu18.04 (nvidia-smi 440.59, CUDA 10.2),

but

when I did make check, my PC turned off. I also tried to install
Gromacs2018.2, Gromacs2018.6 and I have got the same problem. When I

tried

to do mdrun, my PC also shut down. I also tried the following

combination:

nvidia-smi 440.59, CUDA 9.2.

Any ideas would be helpful.

Thanks,
Vlad
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[gmx-users] GROMACS 2020.1 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2020.1 is available!

This first patch release fixes several issues found since the initial 
release of GROMACS 2020. We encourage all users of the 2020
series to update to 2020.1. Please see the link to the release notes 
below for more details.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.1.tar.gz
Documentation: http://manual.gromacs.org/2020.1/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.1.tar.gz

Happy simulating!

Paul

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[gmx-users] GROMACS 2019.6 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2019.6 is available!

The sixth patch release fixes several issues found since the previous 
patch release of GROMACS 2019.

We encourage all users of the 2019 series to update to 2019.6.
Please see the link to the release notes below for more details.

Please note that the 2019 branch is now out of main support, and we will 
only address critical scientific issues in this branch.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2019.6.tar.gz
Documentation: http://manual.gromacs.org/2019.6/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019.6.tar.gz

Happy simulating!

Paul

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Re: [gmx-users] syntax error in GMXRC.csh in Gromacs2020

[Paul Bauer]

Hello,

Please open an issue on redmine for this.

Cheers

Paul

On Mon, 17 Feb 2020, 10:07 Harry Mark Greenblatt, <
harry.greenbl...@weizmann.ac.il> wrote:

> BS”D
>
> Seems that a bash formatted line has made it into the csh version of the
> GMXRC file:
>
> setenv GMXTOOLCHAINDIR=${GMXPREFIX}/share/cmake
>
> The “=“ should be a space.
>
> Harry
>
>
>
>
> 
> Harry M. Greenblatt
> Associate Staff Scientist
> Dept of Structural Biology   harry.greenbl...@weizmann.ac.il
> 
> Weizmann Institute of SciencePhone:  972-8-934-6340
> 234 Herzl St.Facsimile:   972-8-934-3361
> Rehovot, 7610001
> Israel
>
> --
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Re: [gmx-users] generating Doxygen documentation

[Paul Bauer]

The correct address is
http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/doxygen/html-full/index.xhtml

Need to fix a link somewhere then I think.

/Paul

On Wed, 12 Feb 2020, 20:46 Michele Pellegrino,  wrote:

> Moreover: the link to Jenkins does not work (section 7.8.1, "Building the
> documentation"):
>
>
> http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/html-lib/index.xhtml
>
> Cheers,
> Michele
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Michele
> Pellegrino 
> Sent: 12 February 2020 20:39
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] generating Doxygen documentation
>
> Mark,
>
> no such directory is produced after make (evein if the output is 'Built
> target doxygen-all').
> The only Doxyfile I can utilize to generate html/latex documentation is
> 'Doxyfile-compact', while all others are still 'Doxyfile-*.cmakein'.
>
> It seems I need to run cmake somewhere, somehow, but it's not really clear
> to me in which directory (and with which options(s)).
>
> Cheers,
> Michele
> 
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark
> Abraham 
> Sent: 12 February 2020 17:34
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] generating Doxygen documentation
>
> Hi,
>
> When they succeed, the doxygen targets produce files like
>
> $builddir/docs/html/doxygen/html-*/index.xhtml
>
> which you can open in your browser. The doxygen for the released versions
> is on the web however, so it's much easier to just use or refer to that.
>
> Mark
>
> On Wed, 12 Feb 2020 at 16:30, Michele Pellegrino  wrote:
>
> > Hi,
> >
> >
> > I am trying to generate the Doxygen documentation for GROMACS from the
> > files in /docs/doxygen.
> >
> > I following 2020 manual, I run 'make doxygen-all' in the build directory,
> > succesfully; I don't know what to do next: I tried to run cmake in the
> > doxygen directory to generate the Doxyfiles, but I get the following
> errors:
> >
> > """
> >
> > CMake Error at CMakeLists.txt:36 (include):
> >   include could not find load file:
> >
> > gmxCustomCommandUtilities
> >
> >
> > CMake Error at CMakeLists.txt:37 (include):
> >   include could not find load file:
> >
> > gmxOptionUtilities
> >
> >
> > CMake Error at CMakeLists.txt:53 (gmx_dependent_option):
> >   Unknown CMake command "gmx_dependent_option".
> >
> > """
> >
> > What should I do?
> >
> >
> > Thanks for your attention,
> >
> > Michele
> >
> >
> > p.s. I am referring to the github master branch current version
> > --
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Re: [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics

[Paul bauer]

Hello,

you'll need to check if you are properly sampling the different states 
in your simulations,  which should be possible by analyzing the 
histograms you can get from gmx bar -oh


Otherwise you'll need to check if your simulation parameters are 
realistic, as the program warns you :)


Cheers

Paul

On 13/02/2020 21:19, Sadaf Rani wrote:

Dear Gromacs users

I am doing free energy calculation of a ligand with protein. When I do gmx
bar it gives me the following error:-

Temperature: 298.15 K

Detailed results in kT (see help for explanation):

  lam_A  lam_B  DG   +/- s_A   +/- s_B   +/-   stdev   +/-
  0  13.29  0.061.28  0.101.37  0.081.54  0.09
  1  21.41  0.040.47  0.050.31  0.050.77  0.03
  2  30.88  0.060.09  0.020.06  0.010.41  0.06
  3  40.67  0.03   -0.01  0.03   -0.01  0.030.25  0.01
  4  50.50  0.010.11  0.000.10  0.000.22  0.01
  5  60.33  0.01   -0.04  0.01   -0.07  0.030.21  0.03
  6  70.27  0.020.07  0.040.04  0.020.22  0.03
  7  80.11  0.030.05  0.020.04  0.010.16  0.01
  8  90.11  0.01   -0.09  0.02   -0.10  0.020.17  0.01
  9 100.08  0.020.12  0.010.12  0.010.20  0.00
 10 11   -0.04  0.03   -0.01  0.03   -0.01  0.030.18  0.01
 11 12   -0.09  0.030.06  0.030.05  0.030.19  0.02
 12 13   -0.02  0.03   -0.12  0.03   -0.12  0.030.23  0.01
 13 14   -0.01  0.030.17  0.030.16  0.030.28  0.02
 14 15   -0.06  0.03   -0.09  0.03   -0.09  0.030.25  0.01
 15 16   -0.04  0.030.13  0.040.13  0.040.29  0.01
 16 17   -0.15  0.030.04  0.010.04  0.010.24  0.01
 17 18   -0.14  0.030.01  0.020.01  0.020.25  0.01
 18 19   -0.07  0.03   -0.01  0.01   -0.08  0.020.27  0.01
 19 20   -0.05  0.010.18  0.000.09  0.000.28  0.00

WARNING: Some of these results violate the Second Law of Thermodynamics:
  This is can be the result of severe undersampling, or (more likely)
  there is something wrong with the simulations.


Final results in kJ/mol:

point  0 -  1,   DG  8.14 +/-  0.14
point  1 -  2,   DG  3.50 +/-  0.09
point  2 -  3,   DG  2.19 +/-  0.14
point  3 -  4,   DG  1.66 +/-  0.07
point  4 -  5,   DG  1.24 +/-  0.02
point  5 -  6,   DG  0.83 +/-  0.02
point  6 -  7,   DG  0.66 +/-  0.06
point  7 -  8,   DG  0.28 +/-  0.08
point  8 -  9,   DG  0.28 +/-  0.03
point  9 - 10,   DG  0.19 +/-  0.05
point 10 - 11,   DG -0.10 +/-  0.08
point 11 - 12,   DG -0.22 +/-  0.07
point 12 - 13,   DG -0.05 +/-  0.08
point 13 - 14,   DG -0.03 +/-  0.08
point 14 - 15,   DG -0.16 +/-  0.07
point 15 - 16,   DG -0.10 +/-  0.07
point 16 - 17,   DG -0.37 +/-  0.07
point 17 - 18,   DG -0.35 +/-  0.08
point 18 - 19,   DG -0.17 +/-  0.06
point 19 - 20,   DG -0.13 +/-  0.02

total  0 - 20,   DG 17.29 +/-  0.47


I have read in the link that I should not have negative entropy values in
my simulation
https://www.mail-archive.com/gmx-users@gromacs.org/msg55772.html.
Can anyone please suggest me what could be wrong during my simulation and
how should I fix it?

Thank you
Sadaf Rani
Ph.D. visiting student
Lancaster University
Uk



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Re: [gmx-users] Gromacs 2019 - Ryzen Architecture

[Paul bauer]

Hello,

we only added full detection and support for the newer Rizen chip-sets 
with GROMACS 2019.5, so please try if the update to this version solves 
your issue.
If not, please open an issue on redmine.gromacs.org so we can track the 
problem and try to solve it.


Cheers

Paul

On 02/01/2020 13:26, Sandro Wrzalek wrote:

Hi,

happy new year!

Now to my problem:

I use Gromacs 2019.3 and to try to run some simulations (roughly 30k 
atoms per system) on my PC which has the following configuration:


CPU: Ryzen 3950X (overclocked to 4.1 GHz)

GPU #1: Nvidia RTX 2080 Ti

GPU #2: Nvidia RTX 2080 Ti

RAM: 64 GB

PSU: 1600 Watts


Each run uses one GPU and 16 of 32 logical cores. Doing only one run 
at time (gmx mdrun -deffnm rna0 -gpu_id 0 -nb gpu -pme gpu) the GPU 
utilization is roughly around 84% but if I add a second run, the 
utilization of both GPUs drops to roughly 20%, while leaving logical 
cores 17-32 idle (I changed parameter gpu_id, accordingly).


Adding additional parameters for each run:

gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 0 -gpu_id 0 -nb gpu 
-pme gpu


gmx mdrun -deffnm rna0 -nt 16 -pin on -pinoffset 17 -gpu_id 1 -nb gpu 
-pme gpu


I get a utilization of 78% per GPU, which is nice but not near the 84% 
I got with only one run. In theory, however, it should come at least 
close to that utilization.


I suspect, the Ryzen Chiplet design as the culprit since Gromacs seems 
to prefer the the first Chiplet, even if two simultaneous simulations 
have the resources to occupy both. The reason for the 78% utilization 
could be because of overhead between the two Chiplets via the infinity 
band. However, I have no proof, nor am I able to explain why gmx mdrun 
-deffnm rna0 -nt 16 -gpu_id 0 & 1 -nb gpu -pme gpu works as well - 
seems to occupy free logical cores then.


Long story short:

Are there any workarounds to squeeze the last bit out of my setup? Is 
it possible to choose the logical cores manually (I did not found 
anything in the docs so far)?



Thank you for your help!


Best,

Sandro



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Re: [gmx-users] GROMACS 2020 official release

[Paul bauer]

Hello again,

I got notified that there is an issue for the first link, it needs to be 
without the final dot:


http://manual.gromacs.org/2020/release-notes/index.html

Sorry for the inconvenience and happy new year!

Cheers

Paul

On 01/01/2020 18:11, Paul bauer wrote:

Hello GROMACS users!

The official release of GROMACS 2020 is now available.

What new things can you expect? Please see the release notes 
highlights at

http://manual.gromacs.org/2020/release-notes/index.html.

You can find the code, manual, release notes, installation 
instructions and

test suite at the links below.

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz
Documentation: http://manual.gromacs.org/2020/index.html
(includes install guide, user guide, reference manual, and release notes)
Test Suite: 
http://gerrit.gromacs.org/download/regressiontests-2020.tar.gz


Happy simulating!



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[gmx-users] GROMACS 2020 official release

[Paul bauer]

Hello GROMACS users!

The official release of GROMACS 2020 is now available.

What new things can you expect? Please see the release notes highlights at
http://manual.gromacs.org/2020/release-notes/index.html.

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

Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.tar.gz
Documentation: http://manual.gromacs.org/2020/index.html
(includes install guide, user guide, reference manual, and release notes)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.tar.gz

Happy simulating!

--
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GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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Re: [gmx-users] Bilayer exploding with semiisotropic coupling

[Paul Bauer]

Hello,

please upload the log file from the run, as well as the command you used to
run the simulation and your system specs (processor, whether you are using
GPUs).

Then we can see what is wrong here.

Thanks in advance.

Cheers

Paul

On Sat, 4 Jan 2020, 21:14 Kevin Boyd,  wrote:

> Hi,
>
> Can you share more information? Please upload your starting configuration
> and a log file.
>
> On Fri, Jan 3, 2020 at 10:29 AM Namit Chaudhary 
> wrote:
>
> > Hi,
> >
> > Sorry. I didn't realize that attachments aren't uploaded. Below is a link
> > for the files mentioned in the original mail.
> >
> >
> https://drive.google.com/drive/folders/1fUrx4yt3DpCEGY0CACA6n-PXcswfaa31?usp=sharing
> >
> > Namit
> >
> > On Fri, Jan 3, 2020 at 1:12 PM Namit Chaudhary 
> > wrote:
> >
> > > Hi all,
> > >
> > > I am trying to simulate a coarse grain system containing DPPC (10%),
> > > Cholesterol (40%) and a custom lipid that's synthesized by our lab
> (50%,
> > > topology and martini mapping attached).  Our lab uses these molecules
> to
> > > formulate lipid nanoparticles and deliver RNA therapeutics. I am trying
> > to
> > > understand the structure of these nanoparticles. I tried modelling them
> > as
> > > a bilayer but the system seems to be exploding in the z - direction
> > during
> > > the production run if I use semiisotropic or anisotropic pressure
> > coupling
> > > (isotropic coupling seems to work).  Below is the md.mdp file that I am
> > > using.
> > >
> > > integrator   = md
> > > dt   = 0.01
> > > nsteps   = 800
> > > nstcomm   = 100
> > > comm-grps= LIPIDS SOL
> > >
> > >
> > > nstxout  = 0
> > > nstvout  = 0
> > > nstfout  = 0
> > > nstlog   = 1000  ; Output frequency for energies to log
> > > file
> > > nstenergy= 100   ; Output frequency for energies to
> > energy
> > > file
> > > nstxtcout= 1000  ; Output frequency for .xtc file
> > > xtc_precision= 100
> > > xtc-grps =
> > > energygrps   =
> > >
> > >
> > > nstlist  = 10
> > > ns_type  = grid
> > > pbc  = xyz
> > > rlist= 1.1
> > >
> > > coulombtype  = reaction_field  ;Reaction_field (for use
> with
> > > Verlet-pairlist) ;PME (especially with polarizable water)
> > > rcoulomb_switch  = 0.0
> > > rcoulomb = 1.1
> > > epsilon_r= 15 ; 2.5 (with polarizable water)
> > > vdw_type = cutoff  ;cutoff (for use with
> Verlet-pairlist)
> > >
> > > rvdw_switch  = 0.9
> > > rvdw = 1.1 ;1.1 (for use with Verlet-pairlist)
> > >
> > > cutoff-scheme= verlet
> > >
> > > tcoupl   = v-rescale
> > > tc-grps  = LIPIDS SOL
> > > tau_t = 1.0  1.0
> > > ref_t  = 298 298
> > > Pcoupl   = parrinello-rahman
> > > Pcoupltype= semiisotropic
> > > tau_p = 12.0
> > > compressibility   = 3e-4 3e-4  ; 3e-4
> > > ref_p  = 1.0 1.0   ; 1.0 1.0
> > >
> > > gen_vel= yes
> > > gen_temp = 298
> > > gen_seed = 473529
> > >
> > > constraints= none
> > > constraint_algorithm = Lincs
> > > continuation  = no
> > > lincs_order= 4
> > > lincs_warnangle= 30
> > >
> > > Is there something that I can change in my mdp file? Or is there
> > something
> > > wrong with the lipid itself?
> > >
> > >
> > > Thank you
> > > Namit
> > >
> >
> >
> > --
> > *Namit Chaudhary*
> > Chemical Engineering | Carnegie Mellon University
> > M: 724-506-0693 | E: nchau...@andrew.cmu.edu
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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mail to 

Re: [gmx-users] GMX 2020 - COMM Removal Issue

[Paul bauer]

y
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] Gromacs Install problem

[Paul bauer]

Hello,

if you have found a bug in the multi-dimensional array please report it 
on redmine.gromacs.org so we can fix it, together with the build 
configuration that causes it.


Cheers

Paul

On 14/03/2020 00:51, Alexander Tzanov wrote:

The new version from March 2020.1 is buggy. Try version 2020. There is another 
bug in multidimensional array ...

Alex

On Mar 13, 2020 1:54 PM, xuan Zhang  wrote:
Hi,

When I install the Gromacs on Linux, the cmake occurs error like below. I
am a newer on this software. I appreciate very much that you can help me.

Best regards,
Xuan

**/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON
CMake Error at cmake/FindLibStdCpp.cmake:162 (message):
   GROMACS requires C++14, but a test of such functionality in the C++
   standard library failed to compile.  The g++ found at /usr/bin/g++ had a
   suitable version, so ;something else must be the problem
Call Stack (most recent call first):
   CMakeLists.txt:69 (find_package)


-- Configuring incomplete, errors occurred!
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log".
See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log".


*#cmakeerror.log as below:*

Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following
output:
Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f
CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build
make[1]: Entering directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o
/sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++
   -gcc-name=/usr/bin/g++ -DCXX14_COMPILES   -std=c++14 -o
CMakeFiles/cmTC_203a2.dir/src.cxx.o -c
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error:
namespace "std" has no member "cbegin"
   int main() { int a[2]; std::cbegin(a); }
   ^

compilation aborted for
/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2)
CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target
'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed
make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2
make[1]: Leaving directory
'/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp'
Makefile:138: recipe for target 'cmTC_203a2/fast' failed
make: *** [cmTC_203a2/fast] Error 2


Source file was:
#include 
int main() { int a[2]; std::cbegin(a); }

--
*Xuan Zhang*

PhD  Candidate
China University of Petroleum(East China)
School of Petroleum Engineering
No.66 Changjiang West Road, Qingdao


Visiting scholar (2017.12-2018.12)
The University of Texas at Austin
Cockrell School of Engineering
McKetta Department of Chemical Engineering
200 E Dean Keeton St. Stop C0400
CPE 5.428

*(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com
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Re: [gmx-users] Converting a tpr file to an older version of gromacs

[Paul bauer]

Hello,

there is no real supported way of doing this. You would need to 
re-create the TPR in the version you want to use it in.
Can you use an external tool instead of g_mmpbsa that supports reading 
the newer file format?


Cheers

Paul

On 09/04/2020 17:24, Mariem Ghoula wrote:

Hi,

I would like to use g_mmpbsa on my protein-protein complex simulation.
However, after a few errors with the module due to tpr files version
mismatch and after reading some posts with the same issue, I came to the
conclusion that I need to convert my tpr file to an older version. Can you
please help me with this? After installing the old version of gromacs that
is compatible with the g_mmpbsa program, how can I convert my tpr file
issued from an 2019.5 version to an older one (5.0.7)?

Thanks a lot.

- Mariem



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Re: [gmx-users] GROMACS 2020.1 failed to pass make check

[Paul bauer]

Hello,

you are using a plumed modified version that adds extra options to mdrun.
Our unit tests check that the output from mdrun -h stays invariant, and 
this is no longer the case once you modify the code for plumed.


You can ignore this failure in this case, but please mention in the 
future if you are using modified versions of the code.


Cheers

Paul

On 05/04/2020 21:23, Wei-Tse Hsu wrote:

Dear gmx users,
Recently I've been trying to install GROMACS 20201. After successfully
compilng GROMACS 2020.1, when executing make check command, I
encountered the following error. Specifically, one out of 56 tests failed,
which was related to Mdrun Test.WritesHelp. Looking at the error message,
I'm still not sure what it means and how I should solve this problem. I
wonder if anyone had this before that could give me some insights about how
I could solve the problem. Any help would be appreciated!

Here is the error message in the middle.





*[--] 1 test from MdrunTest[ RUN  ]
MdrunTest.WritesHelp/home/wei-tse/Documents/Software/GROMACS/gromacs-2020.1/src/testutils/refdata.cpp:867:
Failure  In item: /Help string   Actual: 'SYNOPSIS*
And here is the error message in the end.





*The following tests FAILED: 43 - MdrunTests
(Failed)CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failedCMakeFiles/Makefile2:1467: recipe for
target 'CMakeFiles/run-ctest-nophys.dir/all'
failedCMakeFiles/Makefile2:445: recipe for target
'CMakeFiles/check.dir/rule' failedMakefile:327: recipe for target 'check'
failed*

And here is the whole STDOUT message of the command printed by make *check

make_check.log*.

https://drive.google.com/file/d/1Nb2BLzA2Vl_cjS1b_M_HNk0wkrfR2WKt/view?usp=sharing

Best,
Wei-Tse



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Re: [gmx-users] Inexpected rmsd

[Paul bauer]

Hello,

you can't attach files here on the mailing list. Please upload the file 
somewhere and share a link to it.


Cheers

Paul

On 27/03/2020 10:35, Jorden Cabal wrote:

Dear Emran Heshmati,
I can not see any graph? Did you attach it. Please verify.
Thank you

On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati  wrote:


I am working on a protein consisting 2 chains. After performing regular MD
simulation and analysis the outputs, I got unexpecter rmsd, as shown in
arttached graph. What is the problem?
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[gmx-users] GROMACS mailing-list will move to a forum

[Paul bauer]

Hello gmx-users!

We have been working behind the scenes the last few months on some 
changes to the organization of the GROMACS project, one of them is 
switching our gmx-users mailing list to a forum


We are continuously re-thinking about how we can best engage with you 
and how people can get the best help when it comes to questions about 
using GROMACS for different scientific problems. While the user list has 
worked well for this in the past, it has also shown some deficiencies, 
mostly in finding already existing questions and the correct answers for 
them. To hopefully change this in the future we are now in the process 
of moving the existing list to use a Discourse forum instead that will 
be made public in the beginning of May. At the switching point, the 
current list will be read only (and the archive will be kept alive) so 
people will still be able to search it in the future for existing 
answers, but won't be able to post any new questions. The forum will 
still support the pure email based conversation if you prefer this kind 
of interaction, but it will also allow ranking of responses and make it 
easier to see which answers are coming from whom.


You will have the opportunity to sign up for the forum when it goes live 
and I'll send a reminder for it when the time comes.


Cheers

Paul

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0046737308594

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Re: [gmx-users] GROMACS 2019-rc1 install issues

[Paul bauer]

Also,

please don't use Release candidate versions for anything serious. 
Instead use the latest official release that suits you.


Cheers

Paul

On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote:

Hi everyone,

I'm a beginner user of GROMACS, and I'm having some troubles with the
installation. I follow the instruction in
http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html ,
but when i run "make", appear the error shown in file attached.
Any advice will be appreciated.

Regards,

Nicolas Rozas Castro
Universidad de Chile, Faculty of Science.



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Re: [gmx-users] GROMACS 2019-rc1 install issues

[Paul bauer]

Hello,

you can't attach files to the list here, either paste the error directly 
from the terminal or upload the file somewhere and share the link.


Cheers

Paul

On 30/03/2020 08:22, Nicolás Marcelo Rozas Castro wrote:

Hi everyone,

I'm a beginner user of GROMACS, and I'm having some troubles with the
installation. I follow the instruction in
http://manual.gromacs.org/documentation/2019-rc1/install-guide/index.html ,
but when i run "make", appear the error shown in file attached.
Any advice will be appreciated.

Regards,

Nicolas Rozas Castro
Universidad de Chile, Faculty of Science.



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[gmx-users] GROMACS 2020.2 patch release available

[Paul bauer]

Hi GROMACS users,

The official release of GROMACS 2020.2 is available!

This second patch release again fixes issues found since the initial 
release of GROMACS 2020 and the release of 2020.1. We encourage all 
users of the 2020
series to update to 2020.2. Please see the link to the release notes 
below for more details.


You can find the code, documentation, release notes, and test suite at 
the links below.


Code: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2020.2.tar.gz
Documentation: http://manual.gromacs.org/2020.2/index.html
(including release notes, install guide, user guide, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.2.tar.gz

Happy simulating!

Paul

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Re: [gmx-users] GROMACS mailing-list will move to a forum

[Paul bauer]

Hello again @ all gmx-users!

A month has passed and we have moved forward with our work to move the 
user mailing list to the [discussion forum] 
https://gromacs.bioexcel.eu/. The discussion forum will open Friday, 8 
May 2020.


We are now ready to accept people signing up to the forum at 
https://gromacs.bioexcel.eu/. We will start allowing new posts starting 
from Friday to give people some time to get used to the forum settings. 
At the same time (Friday), the gmx-users mailinglist will be set in 
read-only mode.


We are looking forward to engaging with you in this new format and hope 
it will help the community to solve user issues with GROMACS.


Cheers

Paul

On 01/04/2020 14:06, Paul bauer wrote:

Hello gmx-users!

We have been working behind the scenes the last few months on some 
changes to the organization of the GROMACS project, one of them is 
switching our gmx-users mailing list to a forum


We are continuously re-thinking about how we can best engage with you 
and how people can get the best help when it comes to questions about 
using GROMACS for different scientific problems. While the user list 
has worked well for this in the past, it has also shown some 
deficiencies, mostly in finding already existing questions and the 
correct answers for them. To hopefully change this in the future we 
are now in the process of moving the existing list to use a Discourse 
forum instead that will be made public in the beginning of May. At the 
switching point, the current list will be read only (and the archive 
will be kept alive) so people will still be able to search it in the 
future for existing answers, but won't be able to post any new 
questions. The forum will still support the pure email based 
conversation if you prefer this kind of interaction, but it will also 
allow ranking of responses and make it easier to see which answers are 
coming from whom.


You will have the opportunity to sign up for the forum when it goes 
live and I'll send a reminder for it when the time comes.


Cheers

Paul



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GROMACS Development Manager
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0046737308594

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Re: [gmx-users] 2020.1: comm broken with -update gpu -bonded gpu ?

[Paul bauer]

Hello,

sorry for the confusion, but I'm currently moving our infrastructure 
over to Gitlab and have set Redmine to read only because of this.


I'll update gmx-users and gmx-developers once the process is done, and 
then you can open the issue on Gitlab using the tracking system there.


Cheers

Paul

On 23/03/2020 19:12, Jochen Hub wrote:

Hi Magnus and Justin,

Am 23.03.20 um 13:52 schrieb Magnus Lundborg:
> Hi Jochen,
>
> Have you tested if this happens with -update cpu? Perhaps it's the 
bonded on GPU that's the problem, unrelated to updating.


The problem only appears with -update gpu, not with -update cpu.

 I didn't see a
> Redmine issue yet. Could you make one?

I tried, but I seem to lack permissions: On

https://redmine.gromacs.org/projects/gromacs/issues/new

I get "You are not authorized to access this page." Did I miss 
something here?


Thanks,
Jochen


Am 23.03.20 um 13:52 schrieb Magnus Lundborg:

Hi Jochen,

Have you tested if this happens with -update cpu? Perhaps it's the 
bonded on GPU that's the problem, unrelated to updating. I didn't see 
a Redmine issue yet. Could you make one?


Cheers,
Magnus

On 2020-03-19 18:01, Jochen Hub wrote:

Hi developers,

I am running a simple DPPC membrane (Berger force field, PME, 1nm 
cutoff, 4fs time step, all standard) with 2020.1 and


comm-mode    = Linear
nstcomm  = 100
comm-grps    = DPPC water  ; OR System

but the membrane rapidly drifts along the z direction: approx. once 
across the box per 100ps, and accelerating over time.


This happens only with

mdrun -update gpu -bonded gpu

but not with

mdrun -update gpu -bonded cpu   (no spelling mistake)

(with a GTX 1070Ti).

Also no problems with 2018.6 or 2019.6.

Seems like the center of mass motion removal is broken when doing 
both *bonded and updating* on the GPU. Is this issue known?


Cheers,
Jochen







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[gmx-users] GROMACS has switched to use Gitlab

[Paul bauer]

Hello gmx users!

I just finished the transition of our project database to use the Gitlab 
servers.


This means that from now on issues should be reported using the issue 
tracker at https://gitlab.com/gromacs/gromacs/-/issues instead of 
redmine.gromacs.org.
The redmine and gerrit servers have been set be read only from now on, 
so that you can still access information there, but it wont be able to 
report new things there any more.


Cheers

Paul

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Re: [gmx-users] GROMACS mailing-list will move to a forum

[Paul bauer]

Hello gmx users!

As announced in my previous message at the beginning of the week, we 
will be activating the new discussion forum today.


At the same time, the mailing list will move to read-only mode, so 
please don't be surprised when it is no longer possible to submit new 
messages to it. :)


As a reminder, you can sign up to the forum here: 
https://gromacs.bioexcel.eu/


Again, we are looking forward to interact with the community in this new 
way, and hope it will make it easier for you to solve issues that you 
have while using GROMACS.


Cheers

Paul

On 04/05/2020 15:51, Paul bauer wrote:

Hello again @ all gmx-users!

A month has passed and we have moved forward with our work to move the 
user mailing list to the [discussion forum] 
https://gromacs.bioexcel.eu/. The discussion forum will open Friday, 8 
May 2020.


We are now ready to accept people signing up to the forum at 
https://gromacs.bioexcel.eu/. We will start allowing new posts 
starting from Friday to give people some time to get used to the forum 
settings. At the same time (Friday), the gmx-users mailinglist will be 
set in read-only mode.


We are looking forward to engaging with you in this new format and 
hope it will help the community to solve user issues with GROMACS.


Cheers

Paul

On 01/04/2020 14:06, Paul bauer wrote:

Hello gmx-users!

We have been working behind the scenes the last few months on some 
changes to the organization of the GROMACS project, one of them is 
switching our gmx-users mailing list to a forum


We are continuously re-thinking about how we can best engage with you 
and how people can get the best help when it comes to questions about 
using GROMACS for different scientific problems. While the user list 
has worked well for this in the past, it has also shown some 
deficiencies, mostly in finding already existing questions and the 
correct answers for them. To hopefully change this in the future we 
are now in the process of moving the existing list to use a Discourse 
forum instead that will be made public in the beginning of May. At 
the switching point, the current list will be read only (and the 
archive will be kept alive) so people will still be able to search it 
in the future for existing answers, but won't be able to post any new 
questions. The forum will still support the pure email based 
conversation if you prefer this kind of interaction, but it will also 
allow ranking of responses and make it easier to see which answers 
are coming from whom.


You will have the opportunity to sign up for the forum when it goes 
live and I'll send a reminder for it when the time comes.


Cheers

Paul





--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594

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