I want to run Upside2-MD for a large conformation, and I am following the instructions on the page. However, when I run the constant temperature simulation, my protein loses its conformation.
Before running the simulation, I prepared my system using the following commands:
Hi,
I want to run Upside2-MD for a large conformation, and I am following the instructions on the page. However, when I run the constant temperature simulation, my protein loses its conformation.
Before running the simulation, I prepared my system using the following commands:
upside_config.py --initial-structure equili.initial.npy --fasta equili.fasta --output simulation.up --rama-library upside2-md-master/parameters/common/rama.dat --rama-sheet-mixing-energy upside2-md-master/parameters/ff_2.1/sheet
For the simulation itself, I used the following command:
upside --duration 1e7 --frame-interval 1e2 --temperature 0.85 --seed $RANDOM simulation.up
Could you please check if I missed something in the instructions?
Regards,
Aashish