GROMACS version:25.2
GROMACS modification: Yes/No
Hi
My workstation equiped with i9 13900 , with 128 GB ram, RTX 5080 16GB and 2 TB nVMe ssd along side cuda 12.9 and ubuntu 24.04
I have a membrane protein system with 600000 atoms, I wanted to perform a 100ns mdrun simulation on it but due to a system instability after every run of 100ns the system freezes due to unknown reasons.
We decided to chunk the 100ns simulation into four 25ns simulations
Please help me if the code being run is correct.
I use previous CPT as input and nsteps to control the time for the same tpr file.
cwd
echo “Running first”
gmx mdrun -v -s step7_1.tpr -deffnm 25ns -nsteps 12500000 -nb gpu -pme gpu -update gpu -ntomp 12
echo “Running second”
gmx mdrun -v -s step7_1.tpr -deffnm 25ns -cpi 25ns.cpt -nsteps 12500000 -nb gpu -pme gpu -update gpu -ntomp 12
echo “Running third”
gmx mdrun -v -s step7_1.tpr -deffnm 25ns -cpi 25ns.cpt -nsteps 12500000 -nb gpu -pme gpu -update gpu -ntomp 12
echo “Running Fourth”
gmx mdrun -v -s step7_1.tpr -deffnm 25ns -cpi 25ns.cpt -nsteps 12500000 -nb gpu -pme gpu -update gpu -ntomp 12
Thanks