SanDisk Membrain Software Manuel d'utilisateur télécharger pdf (Page 37)

3 RUNNING A SIMULATION OF KCSA 37

PMEGridSizeX 80

PMEGridSizeY 80

PMEGridSizeZ 90

}

Note how we carefully chose the Particle Mesh Ewald grid size so as to have

at least one grid point per

A in each direction, and also in such a way that the

number of grid points is a multiple of two, three, or ﬁve.

14 Now ﬁnd the section labeled # Fixed Atoms Constraint. It should look

like:

# Fixed Atoms Constraint (set PDB beta-column to 1)

if {1} {

fixedAtoms on

fixedAtomsFile kcsa_popcwi.fix

fixedAtomsCol B

fixedAtomsForces on

}

This section uses the ﬁle kcsa popcwi.fix to determine which atoms of the

simulated system will be held ﬁxed in space. We will create this ﬁle shortly.

15 Go to the very end of the conﬁguration ﬁle. You should ﬁnd the following

commands:

# Minimization

if {1} {

minimize 1000

reinitvels $temperature

}

run 250000 ;# 0.5 ns

which indicate that NAMD will run 1000 steps of minimization, then it will

reinitiate ve locities according to the desired temperature, and then it will run

dynamics for 0.5 ns (using a 2 fs timestep).

16 Close the text editor.

Before performing the simulation, we need to generate a ﬁle indicating which

atoms will be ﬁxed.

17 Open VMD and type in the Tk Console:

1 2 ... 32 33 34 35 36 37 38 39 40 41 42 43

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SanDisk Membrain Software Manuel d'utilisateur Page 37