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

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

Re: [gmx-users] Specbond.dat file

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

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

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

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

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

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

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

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

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

[gmx-users] GROMACS 2018.3 patch release available

/download/regressiontests-2018.3.tar.gz Happy simulating! Paul Bauer GROMACS Release Manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Gromacs 2018.3 install warning

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`

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

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

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

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

Re: [gmx-users] trjconv ndec not working

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

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

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

[gmx-users] First beta release of 2019

ease-notes/index.html Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019-beta1.tar.gz Happy testing! Paul Bauer GROMACS release manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

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

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

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

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

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

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.

[gmx-users] GROMACS 2018.4 patch release available

/download/regressiontests-2018.4.tar.gz Happy simulating! Paul Bauer GROMACS Release Manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Second beta release of GROMACS 2019

ease-notes/index.html Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019-beta2.tar.gz Happy testing! Paul Bauer GROMACS release manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] GROMACS 2019 official release

. 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

[gmx-users] GROMACS 2018.5 patch release available

/regressiontests-2018.5.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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

Re: [gmx-users] Make errors 2019rc1

. 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

[gmx-users] GROMACS 2019 release candidate

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: http://gerrit.gromacs.org/download/regressiontests-2019-rc1.tar.gz Happy testing! Paul Bauer GROMACS relea

Re: [gmx-users] Make errors 2019rc1

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:

Re: [gmx-users] Running Grompp in reverse and backing up MD data

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.

[gmx-users] Third beta release of GROMACS 2019

index.html Test Suite: http://gerrit.gromacs.org/download/regressiontests-2019-beta3.tar.gz Happy testing! Paul Bauer GROMACS release manager -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Bond breakage modelling

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

[gmx-users] GROMACS 2018.6 patch release available

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

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

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

[gmx-users] GROMACS 2016.6 patch release available

/regressiontests-2016.6.tar.gz Happy simulating! Paul Bauer -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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

[gmx-users] GROMACS 2019.1 patch release available

://gerrit.gromacs.org/download/regressiontests-2019.1.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] GROMACS 2019.1 patch release available

: http://gerrit.gromacs.org/download/regressiontests-2019.2.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

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

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

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

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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please

[gmx-users] GROMACS 2018.7 patch release available

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

[gmx-users] GROMACS 2019.3 patch release available

: http://gerrit.gromacs.org/download/regressiontests-2019.3.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

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

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!

Re: [gmx-users] There is no domain decomposition 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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab

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

=ON’. OR Are there other things that can be checked or done to make the gromacs use GPU acceleration. Any help would be appreciated. -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] gromacs make check failure

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 -- Gromacs Users mailing list * Please search

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

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

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

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

Re: [gmx-users] About 2019 GMX manual

: 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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list

[gmx-users] GROMACS 2019.4 patch release available

Suite: http://gerrit.gromacs.org/download/regressiontests-2019.4.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

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

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

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

se check the GROMACS website at http://www.gromacs.org/Documentation/Errors application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www

[gmx-users] Webinar on mdp file settings

://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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm

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

v. 2019.4. I would appreciate some help, thank you, Vangelis. -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

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

[file dna-his_DNA_chain_J.itp, line 44148]: No default Improper Dih. types -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

[gmx-users] Third beta release of GROMACS 2020

2020-beta3/release-notes/index.html Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020-beta3.tar.gz Happy testing! -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.o

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

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

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

* 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. -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] Fwd: gmx trjcat

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 -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737

Re: [gmx-users] Fwd: gmx trjcat

: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

Re: [gmx-users] regression test errors

'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

Re: [gmx-users] regression test errors

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

Re: [gmx-users] regression test errors

') 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

Re: [gmx-users] regression test errors

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

[gmx-users] Second beta release of GROMACS 2020

.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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-

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

-09-24/ Cheers Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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

[gmx-users] First beta release of GROMACS 2020

umentation/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 -- Gromacs Users mailing list * Please search the archiv

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

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 -- Paul Bauer

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

University of Alberta Department of Electrical and Computer Engineering, 4-021 ECERF Edmonton, AB, T6G 2G8 Canada Email: dor...@ualberta.ca -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list

[gmx-users] GROMACS 2018.8 patch release available

.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Release Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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

[gmx-users] GROMACS 2020 release candidate

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

[gmx-users] GROMACS 2019.5 patch release available

/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 -- Paul Bauer, PhD GROMACS Release

Re: [gmx-users] GROMACS 2020 release candidate

--- 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

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

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

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

this? Regards, Andreas -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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

Re: [gmx-users] install and mdrun problems

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. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm

[gmx-users] GROMACS 2020.1 patch release available

: http://gerrit.gromacs.org/download/regressiontests-2020.1.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] GROMACS 2019.6 patch release available

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

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

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

Re: [gmx-users] generating Doxygen documentation

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,

Re: [gmx-users] how to fix error: Some of these results violate the Second Law of Thermodynamics

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 -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm

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

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 -- Paul Bauer, PhD GROMACS Develop

Re: [gmx-users] GROMACS 2020 official release

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

[gmx-users] GROMACS 2020 official release

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

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

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

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

requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Suppo

Re: [gmx-users] Gromacs Install problem

n)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archiv

Re: [gmx-users] Converting a tpr file to an older version of gromacs

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

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

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 -- Paul Bauer

Re: [gmx-users] Inexpected rmsd

/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. -- Paul Bauer, PhD GROMACS

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

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 -- Gromacs Users mailing list * Please search the archive at http

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

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

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

of Science. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- 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/Mai

[gmx-users] GROMACS 2020.2 patch release available

, reference manual) Test Suite: http://gerrit.gromacs.org/download/regressiontests-2020.2.tar.gz Happy simulating! Paul -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

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

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

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

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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Sup

[gmx-users] GROMACS has switched to use Gitlab

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

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

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