GROMACS version:2020.1
GROMACS modification: No
when I follow the tutorial (2) to run the program, it processed to generate “strong_posre.itp”, an errors occurs:
Reading sturcture file
Select group to position restrain
Segmentation fault(core dumped)
Hi,
Please provide more information on the problem, command-line that gives error with all the option and the error you got.
Best regards
Alessandra
This is a known bug that has been fixed. Upgrade to 2020.4 and try again.
Thank you very much. I checked my gromacs program. I find that I downloaded version 2020.4, but when I finished the installation, use gmx --version to check the version number, and give a prompt message: 2020.1-ubuntu-2020.1-1. I dont konw where the problem is？
Best regards.
When I preform the simulation according to the website “KALP-15 in DPPC”. It proceeds to generate the “strong_posre.itp” file (using the command “gmx genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000”) Then, an error occurs:
Reading sturcture file
Select group to position restrain
Segmentation fault(core dumped).
And I use VMD to check my structure, There is no problem.
Thanks.
You need to uninstall the 2020.1 package that you installed via the package manager, compile and install 2020.4 from source, and add the 2020.4 installation to your PATH. The installation instructions in the manual explain how to do that.
Thank you, Sir.
I used the following command to install Gromacs 2020.4.
“tar xfz gromacs-2020.4.tar.gz
cd gromacs-2020.4
mkdir build
cd build
cmake … -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC”
Can’t I use this installation method？
Best regerds
That is a minimal build process that may work if all the required components are in the default locations. You still have to uninstall the 2020.1 Ubuntu package before you can use 2020.4, because /usr/bin (where Ubuntu installs the gmx binary) comes first in the $PATH before /usr/local/gromacs/bin.