Step Four: Energy Minimization
The job.sh script I provide for running these calculations will create the following directory hierarchy: Lambda_0/ Lambda_0/EM/ Lambda_0/NVT/ Lambda_0/NPT/ Lambda_0/Production_MD/ This way, all steps in the workflow are executed within a single directory for each value of init_lambda_state. I find this to be a convenient way to organize the jobs and their output. The script also assumes that the .mdp files are also organized hierarchically within some directory $MDP/ $MDP/EM/ $MDP/NVT/ $MDP/NPT/ $MDP/Production_MD/ As described before, energy minimization will be conducted using the steepest descent method. The relevant section in the job.sh script is: mkdir Lambda_$LAMBDA cd Lambda_$LAMBDA ################################# # ENERGY MINIMIZATION 1: STEEP # ################################# echo "Starting minimization for lambda = $LAMBDA..." mkdir EM cd EM # Iterative calls to grompp and mdrun to run the simulations gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/methane_water.gro -p $FREE_ENERGY/topol.top -o min$LAMBDA.tpr gmx mdrun -deffnm min$LAMBDA echo "Minimization complete."
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