Installation Error

[erolic]

I am trying to install gromacs-ramd-release-2023 version with the following command;

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=CUDA -DCMAKE_C_COMPILER=gcc-10 -DCMAKE_CXX_COMPILER=g++-10

with Cuda compilation tools, release 11.5, V11.5.119

however i am getting following error;

/home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp: In constructor ‘gmx::RAMD::RAMD(const gmx::RAMDParams&, pull_t, int64_t, gmx::StartingBehavior, const t_commrec, int, const t_filenm, const gmx_output_env_t, FILE)’: /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:89:9: error: ‘MASTER’ was not declared in this scope 89 | if (MASTER(cr) and opt2bSet("-ramd", nfile, fnm)) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp: In member function ‘virtual void gmx::RAMD::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput)’: /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:119:9: error: ‘MASTER’ was not declared in this scope 119 | if (MASTER(cr) and out and (pstep % params.eval_freq == 0)) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:132:17: error: ‘MASTER’ was not declared in this scope 132 | if (MASTER(cr) and out) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:143:13: error: ‘MASTER’ was not declared in this scope 143 | if (MASTER(cr) and debug) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:155:17: error: ‘MASTER’ was not declared in this scope 155 | if (MASTER(cr) and debug) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:167:17: error: ‘MASTER’ was not declared in this scope 167 | if (MASTER(cr) and out) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:178:21: error: ‘MASTER’ was not declared in this scope 178 | if (MASTER(cr)) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:192:17: error: ‘MASTER’ was not declared in this scope 192 | if (MASTER(cr) and debug) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:207:21: error: ‘MASTER’ was not declared in this scope 207 | if (MASTER(cr) and debug) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:219:9: error: ‘MASTER’ was not declared in this scope 219 | if (MASTER(cr) and (pstep % params.eval_freq == 0)) | ^~ /home/bau/Downloads/gromacs-ramd-release-2023/src/gromacs/ramd/ramd.cpp:114:54: warning: unused parameter ‘forceProviderOutput’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wunused-parameter-Wunused-parameter]8;;] 114 | ForceProviderOutput forceProviderOutput) | ~~~~~~^~~~~~~ At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-cast-function-type-strict’ may have been intended to silence earlier diagnostics make[2]: [src/gromacs/CMakeFiles/libgromacs.dir/build.make:5634: src/gromacs/CMakeFiles/libgromacs.dir/ramd/ramd.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:4331: src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 make: *** [Makefile:166: all] Error 2

i could not figure out what is wrong. could you please check?

[BerndDoser]

Thanks for the report. I will check it.

[BerndDoser]

Sorry for the late reply. I just realized that you are trying to compile gromacs-ramd-2023. This version is not released yet and still under development. The latest stable version is gromacs-2020.5-ramd-2.0. There is also a release candidate available gromacs-2022.5-ramd-2.1-rc1. Further updates are planned for next year at the earliest.

[amarye]

Hi @BerndDoser I have compiled GROMACS-RAMD 2022.5 and used the 3htb structure with the jz4 ligand. I have also modified the ligand name in the MDP file. However, I encountered an error. Could you please tell me why?.
I'm wondering if there is a newer version available.

![Uploading Screenshot from 2024-04-02 11-07-15.png…]()

[BerndDoser]

The annual updates up to GROMACS 2024 are available in the corresponding branches. For the official release of "GROMACS-2022.6-RAMD-2.1" and subsequent versions, I also need to wait for permission from the scientific users. For your specific issue, I need additional details. The screenshot appears to be broken.

[amarye]

The annual updates up to GROMACS 2024 are available in the corresponding branches. For the official release of "GROMACS-2022.6-RAMD-2.1" and subsequent versions, I also need to wait for permission from the scientific users. For your specific issue, I need additional details. The screenshot appears to be broken.

I have recompiled gromacs-RAMD 2024. I have used complex system, i.e. protein (3HTB) and ligand (JZ4). I have preformed energy minimization and NVT/NPT equilibrations. For RAMD simulation, I have used npt.tpr, npt.cpt, index.ndx, ramd.mdp (I have modified for LIG), and toppol.top, but I got error. The error stated that Group INH in mdp file was not in the list of index file. As I know INH ligand is the ligand from the RAMD tutorial at kbbox.h-its.org, so I am confused why I got this error.

error.zip

[BerndDoser]

Please use the new MDP parameters introduced in RAMD v2 (see https://github.com/HITS-MCM/gromacs-ramd/issues/15). Since the correct MDP parameter 'ramd-group1-ligand' is not found, the default value 'INH' is used.

[amarye]

Please use the new MDP parameters introduced in RAMD v2 (see #15). Since the correct MDP parameter 'ramd-group1-ligand' is not found, the default value 'INH' is used.

Thank you. It's working now.

[BerndDoser]

You're welcome. Thank you for using RAMD!