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
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
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
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
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
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
/download/regressiontests-2018.3.tar.gz
Happy simulating!
Paul Bauer
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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`
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
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
simu
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
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
ease-notes/index.html
Test Suite:
http://gerrit.gromacs.org/download/regressiontests-2019-beta1.tar.gz
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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
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
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.
/download/regressiontests-2018.4.tar.gz
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*
.
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)
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/regressiontests-2018.5.tar.gz
Happy simulating!
Paul
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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
tion: 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:
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GROMACS relea
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:
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.
index.html
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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
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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
/regressiontests-2016.6.tar.gz
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Paul Bauer
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Paul
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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
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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: http://gerrit.gromacs.org/download/regressiontests-2019.3.tar.gz
Happy simulating!
Paul
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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!
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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=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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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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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
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
:
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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Suite: http://gerrit.gromacs.org/download/regressiontests-2019.4.tar.gz
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Paul
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ile 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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se 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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://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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v. 2019.4.
I would appreciate some help,
thank you,
Vangelis.
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* Can't
[file dna-his_DNA_chain_J.itp, line 44148]:
No default Improper Dih. types
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2020-beta3/release-notes/index.html
Test Suite:
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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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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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0046737
: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
'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
ithout 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
') 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
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
.html
Test Suite:
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-09-24/
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Test Suite:
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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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.tar.gz
Happy simulating!
Paul
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py testing!
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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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---
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
-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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this?
Regards,
Andreas
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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
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,
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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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,
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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
simulating!
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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
requests visit
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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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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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Paul Bauer
/Support/Mailing_Lists/GMX-Users_List before
posting!
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Paul Bauer, PhD
GROMACS
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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Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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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.
--
Paul
of Science.
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Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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, reference manual)
Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.2.tar.gz
Happy simulating!
Paul
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Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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http://www.gromacs.org/Support
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
of mass motion removal is broken when doing
both *bonded and updating* on the GPU. Is this issue known?
Cheers,
Jochen
--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
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Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Sup
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
--
Paul Bauer, PhD
GROMACS Development Manager
KTH Stockholm, SciLifeLab
0046737308594
--
Gromacs Users mailing list
* Please search
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
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