Energy minimization error sc-r-power = 48 not supported

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1

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GROMACS modification: Yes/No
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Dear Gromacs Community,

I am getting the following error during energy minimization of my system using Gromacs 2022.1 version. I appreciate your help.

I used the following command : gmx_mpi mdrun -v -deffnm em
ERROR:
fatal error
gromacs/2022.1 does not support sc-r-power = 48.

System: My system contains ~2000 Proteins, 2 RNA chains, ~2000 ZN+2 ions, 30 million water tip3p and 5000 Chloride ions.

I tried two different things and none of these have worked:

  1. I assigned the value of sc-r-power = 6 in the minim.mdp file while preparing em.tpr.
    It gave me the same error as above.
  2. I prepared and ran the simulation with gromacs/2019.6 mdrun_mpi. this gave me a different error:
    Memory allocation failed:
    std::bad_alloc
2

With which GROMACS version did you prepare the tpr for 2022.1?

I recall having seen this issue before, but I don’t recall the cause of it. I think it should work when using grompp from 2022.1. Otherwise a newer 2022 patch release should certainly work.

3

Hello,

Thanks for the response. I will try using the newer patches.
I got the sc-r-power=48 not supported error message when I prepare tpr file using gromacs/2022.1
I also tried 2019.6 and 2020.1 version to prepare tpr file but they give bad memory allocation error.

I could run md on the same protein system without RNA and ZN+2 but I get these errors when I put RNA and zn+2 into the system.

4

:-) GROMACS - gmx mdrun, 2024.4 (-:

Executable: /home/gromacs_2024.4_13_NOV/bin/gmx_mpi
Data prefix: /home/gromacs_2024.4_13_NOV
Working dir: /home/trial
Command line:
gmx_mpi mdrun -v -deffnm nvt_annealing -nsteps 4500000 -append -cpi nvt_annealing.cpt

Reading file nvt_annealing.tpr, VERSION 2024.4 (single precision)

Program: gmx mdrun, version 2024.4
Source file: src/gromacs/fileio/tpxio.cpp (line 572)
MPI rank: 0 (out of 288)

Fatal error:
Only sc-r-power=6 is supported. Value in file is 0.000000

For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.4 documentation

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

I encountered the same error while using 2024.4 version of gromacs. Please guide me through this. Should I use different version of 2024 instead of the latest?

5

Yes, there is an, unintended, incompatibility of older tpr files when certain features are used. Using GROMACS 2024 for generating the tpr file should solve the issue. 2023 might also work.