Re: [gmx-users] gromacs 2020, bug? high total energy

Hi, It was not gromacs 2020, but my fault and mixing up various tools (grompp, mdrun) from 2019 and 2020 versions. I am sorry. Bests, Tamas On 4/14/20 4:44 PM, Tamas Hegedus wrote: Hi, There might be some bug(?) in gromacs 2020. I can not decide. I just installed 2020.1 today using the sam

[gmx-users] gromacs 2020, bug? high total energy

Hi, There might be some bug(?) in gromacs 2020. I can not decide. I just installed 2020.1 today using the same script (and libraries) what I have used for gromacs 2019. After energy minimization, in the nvt equilibration run, it stops: Fatal error: Step 0: The total potential energy is 1.99295

Re: [gmx-users] Gromacs 2020

Hi, The code is tested extensively on a range of compilers, so we believe it is correct and compliant. In particular, you're using gcc 6.1.0 and GROMACS tests with 6.4.0, so the issue might have been fixed in the meantime. As newer versions of gcc and cuda will give better performance, I suggest y

[gmx-users] Gromacs 2020

Hi all After attempting to install GROMACS 2020 on new system, I get the error below. The system details & other details are below the error. cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/home/b5018993/src/gromacs-2020 -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_

Re: [gmx-users] Gromacs 2020 fails to run adh_cubic_vsites

Den 2020-03-07 kl. 17:04, skrev Rolly Ng: Dear Gromacs developers, I am new to Gromacs and I have recently compiled Gromacs 2020. I tried to run the ADH benchmarks from ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz The adh_cubic and adh_dodec completed successful

[gmx-users] Gromacs 2020 fails to run adh_cubic_vsites

Dear Gromacs developers, I am new to Gromacs and I have recently compiled Gromacs 2020. I tried to run the ADH benchmarks from ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites and adh_dodec_vsites

[gmx-users] Gromacs 2020 fails to run adh_cubic_vsites

Dear Gromacs developers, I am new to Gromacs and I have recently compiled Gromacs 2020. I tried to run the ADH benchmarks from ftp://ftp.gromacs.org/pub/benchmarks/ADH_bench_systems.tar.gz The adh_cubic and adh_dodec completed successfully, but the adh_cubic_vsites and adh_dodec_vsites

Re: [gmx-users] gromacs-2020 build gcc/nvcc error

Dear Ryan, On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you so much for your help. I performed the following steps > and it seems to have built successfully, I'll let you know if it does not > run correctly as well. > > rm -r gromacs-2020/ > sudo apt-get

Re: [gmx-users] gromacs-2020 build gcc/nvcc error

Dear Szilárd, Thank you so much for your help. I performed the following steps and it seems to have built successfully, I'll let you know if it does not run correctly as well. rm -r gromacs-2020/ sudo apt-get install gcc-8 g++-8 tar -xvzf gromacs-2020.tar.gz cd gromacs-2020/ mkdir build

Re: [gmx-users] gromacs-2020 build gcc/nvcc error

Dear Ryan, On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you for your quick response. You are correct, after > issuing sudo apt-get install gcc-9 g++-9 CMake was run with: > gcc 9 is not supported with CUDA, as far as I know version 8 is the latest suppor

Re: [gmx-users] gromacs-2020 build gcc/nvcc error

Dear Szilárd, Thank you for your quick response. You are correct, after issuing sudo apt-get install gcc-9 g++-9 CMake was run with: CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cud

Re: [gmx-users] gromacs-2020 build gcc/nvcc error

Hi Ryan, The issue you linked has been worked around in the build system, so my guess is that the issue you are seeing is not related. I would recommend that you update your software stack to the latest version (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should be able to g

[gmx-users] gromacs-2020 build gcc/nvcc error

Hello Gromacs experts, First things first, I apologize for any double post but I just joined the community so I'm very new and only found 1-2 posts related to my problem but the solutions did not work. I have been doing MD for about 6-months using NAMD but want to also try out Gromacs. T

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! The

[gmx-users] GROMACS 2020 official release

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

Re: [gmx-users] GROMACS 2020 release candidate

. 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

Re: [gmx-users] GROMACS 2020 release candidate

; 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

[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.