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2 PLACING KCSA IN A MEMBRANE 32

solv remove.tcl.

Now we will use the Autoionize Plugin, which creates a speciﬁed ionic concen-

tration of either KCl or NaCl by transmuting random water molecules into ions.

The plugin also neutralizes the system, which is important for NAMD’s long-

range e lectrostatics to work properly. Note that the ionization of your system

must be done when everything else (protein, membrane, water) is ready.

7 Select Extensions → Modeling → Add Ions in the VMD Main window, then

enter the following parameters:

Option Setting

Input PSF kcsa popcw.psf

Input PDB kcsa popcw.pdb

Output preﬁx kcsa popcwi

Concentration 0.4

Neutralize Yes

Min. distance from molecule 5

Min. distance between ions 5

Segment ID ION

Switch to KCl Yes

Then click Autoionize and wait a minute or two. It’s that simple! Note

that we have used 0.2 M KCl as the ionic concentration of our system

(0.2 × 2).

8 Load the output ﬁles of autoinize (kcsa popcwi.psf and kcsa popcwi.pdb)

into VMD and check that the ions are really there and that the system is

neutral (Fig. 10).

Ionic concentration. Living organisms tightly control the concen-

tration of ions inside and outside of cells. Therefore, you must set

up the right ion concentration for your simulated system guided by

the corresponding physiological or experimental conditions in which

your protein works (usually between 50 to 100 mM for standard

monovalent ions).

Finally, after all of this work, we are ready for minimization and equilibration

with NAMD. This is described in the next unit.

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SanDisk Membrain Software Manual do Utilizador Página 32