How can i get the exchange probabiltiy?

User discussions
1

GROMACS version:2020.4

i installed gromacs and need to know the exchange probability but didn’t got any file holding this name and got only md.log which also didn’t contain exchange probability

this the command i run for 36 temperatures

for i in 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
do
gmx grompp -f nvt_$i.mdp -c em.gro -p topol.top -o remd_$i.tpr
done
gmx mdrun -ntmpi 18 -ntomp 2 -dds 0.998 -s remd_$i.tpr

does exchange probability appears after run finish or during the run ?

2

Are you intending to run replica exchange MD? Your commands above loop over grompp then run a single mdrun process. You do not run REMD simulations in a loop, there is specific syntax (see the manual and online tutorials).

1 Like
3

Excuse me do you mean I need to write the single command in the loop … and where can I find the tutorial for this point.

Thanks a lot for replying

4

https://www.gromacs.org/Documentation_of_outdated_versions/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B

1 Like
5

thanks a lot for helping . i followed the tutorial as i have now 6 temperatures … i created folder called stage2 inside it i created 6 folders each one called sim1 sim2 … sim6 inside each folder sim.mdp with the temperature and sim.tpr

i run this command

mpirun -np 6 gmx_mpi mdrun -ntomp 12 -v -multidir sim[123456] -replex 100
but got
gmx_mpi: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory
gmx_mpi: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory
gmx_mpi: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory
gmx_mpi: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory
gmx_mpi: error while loading shared libraries: libcufft.so.9.1: cannot open shared object file: No such file or directory

It seems that [at least] one of the processes that was started with
mpirun did not invoke MPI_INIT before quitting (it is possible that
more than one process did not invoke MPI_INIT – mpirun was only
notified of the first one, which was on node n0).

mpirun can only be used with MPI programs (i.e., programs that
invoke MPI_INIT and MPI_FINALIZE). You can use the “lamexec” program
to run non-MPI programs over the lambooted nodes.

6

You need to configure your environment to find the CUDA libraries.