Correct Setup for Temperature Replica Exchange (T-REMD) in GROMACS Without PLUMED

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1

GROMACS version: 2024.4
GROMACS modification: Yes/No
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I have a question regarding temperature replica exchange (T-REMD) in GROMACS (without using PLUMED).

After completing energy minimization, NVT, and NPT equilibration using the same temperature, I plan to specify the desired temperatures and create multiple directories, each containing a replex.mdp file with the corresponding temperature.

I defined:

  • TEMP_DIR = Variable name representing directories named according to their respective temperatures (e.g., 298.00/, 300.60/, etc.).

Is this the correct procedure to run T-REMD (without PLUMED)?

  1. Generate TPR files for each temperature:

for TEMP_DIR in 298.00 300.60 303.23 305.8; do
gmx grompp -f TEMP_DIR/replex.mdp
-c npt.gro
-p topol.top
-o TEMP_DIR/tremd.tpr
-r npt.gro
-maxwarn 3
done

  1. mpirun -np 60 gmx_mpi mdrun -v -deffnm tremd -multidir 298.00 300.60 303.23 305.8 -replex 1000
2

Yes, apart from that you need to add the -replex option to mdrun.