Loop over Distance

MDP:

Once the system is well equilibrated, the system is simulated at various distances between the C240s. One of the molecules is fixed at a position with a soft harmonic potential and the other molecule is pulled towards it maintaining a distance =”DISTANCE”. The spring constant is decided such that molecule 1 can move 0.5 Å in the z direction but in x and y direction it can move only 0.1 Å . Similarly, molecule 2 is fixed at position with a relaxation of 0.1 Å . The pull option for mdp is:

pull = yes
pull-ngroups = 2
pull-group1-name=C24_1
pull-group2-name = C24_2
pull-ncoords = 3
pull-nstxout=50
pull-nstfout=50

pull-coord1-type = umbrella
pull-coord1-geometry = direction-periodic
pull-coord1-groups = 1 2
pull-coord1-vec = 0 0 1
pull-coord1-init=DISTANCE
pull-coord1-dim = N N Y
pull-coord1-k = 1000

the other coordinates of pull option is similar to NPT.

JOB SCRIPT

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The job script “prodLoop.sh” consists of a “while” loop that does the following tasks:

• use basic calculator to calculate the DISTANCE for the mdp file
• use sed to overwrites the “DISTANCE” in the mdp file with the value evaluated
• runs the simulation starting with the .gro file from the previous run