I tested my system with different ligands to follow the tutorial and when I typed prepare_dual_topology.py --config_file=step2.ini, my computer rebooted later before the command was finished. I checked the status of my CPU% and found that the core used varied continuously to a maximum of 3200%, I'm not sure if the crash was related to this. I have changed allcpus to different numbers but the CPU% was still the same. I'm using Ubuntu 22.04.3 with the CPU of AMD 7950X, which has 16 cores and 32 threads.
Here is the output of the screen and Molecule information was omitted:
=============mdp and run steps===============
Complex Water
min01.mdp min01.mdp
min02.mdp min02.mdp
min03.mdp nve.mdp
nve.mdp nvt.mdp
nvt.mdp npt.mdp
npt.mdp md.mdp
md.mdp -
============= Input ligands ==============
Name Molecule Topology
LIG0 lig_data/LIG0.itp
LIG1 lig_data/LIG1.itp
LIG2 lig_data/LIG2.itp
LIG3 lig_data/LIG3.itp
============ Perturbations ===========
State A State B
LIG0 LIG1
LIG0 LIG2
LIG0 LIG3
========= Poses read ===========
Name File Details
LIG0 {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x14d603d1b150>, 'topology': ['ligdata/LIG0.itp']}
=============== Superimposed poses ===============
Name File Note
I tested my system with different ligands to follow the tutorial and when I typed
prepare_dual_topology.py --config_file=step2.ini, my computer rebooted later before the command was finished. I checked the status of my CPU% and found that the core used varied continuously to a maximum of 3200%, I'm not sure if the crash was related to this. I have changed allcpus to different numbers but the CPU% was still the same. I'm using Ubuntu 22.04.3 with the CPU of AMD 7950X, which has 16 cores and 32 threads. Here is the output of the screen and Molecule information was omitted: =============mdp and run steps=============== Complex Watermin01.mdp min01.mdp
min02.mdp min02.mdp
min03.mdp nve.mdp
nve.mdp nvt.mdp
nvt.mdp npt.mdp
npt.mdp md.mdp
md.mdp -
============= Input ligands ============== Name Molecule Topology
LIG0 lig_data/LIG0.itp LIG1 lig_data/LIG1.itp LIG2 lig_data/LIG2.itp LIG3 lig_data/LIG3.itp ============ Perturbations =========== State A State B
LIG0 LIG1
LIG0 LIG2
LIG0 LIG3
========= Poses read =========== Name File Details
LIG0 {'molecule': <rdkit.Chem.PropertyMol.PropertyMol object at 0x14d603d1b150>, 'topology': ['ligdata/LIG0.itp']}
=============== Superimposed poses =============== Name File Note