Hello Researchers,
I am trying to extend my MD simulation using command " gmx_mpi convert-tpr -s MD.tpr -extend 50000000 -o MD_20.tpr" but getting error as gmx_mpi command not found.
Can someone help me with step wise solution for this, or any other method by which I can extend my MD simulations.
I am using WSl and ubuntu 20.04
with specs:
GROMACS version: 2023.2
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NB cluster size: 8
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 9.4.0
CUDA driver: 12.40
CUDA runtime: 11.80
Hello @Chintan,
By the look of it, you have compiled GROMACS with MPI library: thread_mpi, not with OpenMPI, so you should call GROMACS commands as gmx not gmx_mpi, e.g. gmx convert-tpr ....
Please check the errors, they are very informative! In this case the flag -no is not recognised by GROMACS. This is because the correct flag to stop the appending is -noappend, without the space between no and append. Hope this helps!
Thank You so much, It helped to run the command but still my MD run is not getting extended, it is starting from 0 step.
I want to extend my gmx run that i first run till 200 ns steps. Now U want to increase it to 50 ns more. i tries everything but still my MD runs are starting from step 0. Can you help me in this ?
You should take your time and read here and there how to extend simulations, e.g. here.
First of all, you are extending your simulations by 50000000 steps (50 MILLIONS). The -extend flag extends the simulations by an amount in ps, so you are asking for 50 * 10⁶ ps, which is a ridiculous amount of time. This is also reported by the output you posted, where it says Runtime for the run 5.02e+07 ps. You want to change the flag value to -extend 50000, which are 50000ps=50ns.
Your command to continue the simulation is correct, i.e., the updated .tpr and the pointing to the previous .cpt file. It may be starting from zero maybe because the extend time is so long that there is some error somewhere?
May be I have tried many methods, so overwriting of files happened, I will try it again after restoring the previous files. Let see if it can be resume again. And I can manage longer rungs as I have good GPU with performance of 125 %. I let here know if something came up, really thanks for your help.
Thank you so much!! Love from India.