SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 41)

3 RUNNING A SIMULATION OF KCSA 41

Pumping out water. The keep water out.tcl Tcl script auto-

matically applies forces to water molecules entering the membrane

hydrophobic region. The script makes use of the NAMD Tcl Forces

module. We encourage you to look at the script, use it, and modify

it to suit your needs. A detailed description of the script can be

found in the “User-Deﬁned Forces in NAMD” tutorial. Note how

we modify it to exclude water molecules present in KcsA cavities.

Before performing the s imulation, we need to generate a ﬁle for the harmonic

constraints on the protein.

8 Open VMD and type in the Tk Console:

mol new ../02-MEMBRANE/kcsa popcwi.psf

mol addfile ../02-MEMBRANE/kcsa popcwi.pdb

set all [atomselect top "all"]

$all set beta 0

set prot [atomselect top "protein"]

$prot set beta 1

$all writepdb kcsa popcwi.cnst

exit

Here we used the coordinates stored in kcsa popcwi.pdb because in the

previous run all protein atoms were ﬁxed. Otherwise, we would have used

the restart ﬁle kcsa popcwimineq-01.restart.coor instead.

The commands you typed above created a ﬁle, kcsa popcwi.cnst, that con-

tains zeros in the B eta ﬁeld of all atoms except those that belong to the protein,

which contain a 1. The latter value corresponds to the spring constant “k”

of the applied harmonic constraint in kcal/mol/

. Note that you can easily

estimate how much atoms will move around their constrained position by using

the equipartition theorem and a given spring constant:

∼

⇒ ∆x ∼

(1)

9 Run your simulation using NAMD2. Usual NAMD installations will ac-

cept the command line

namd2 kcsa popcwimineq-02.conf > kcsa popcwimineq-02.log

in a terminal window.

3.3 Equilibration with Protein Released

After minimization and equilibration with the protein constrained, we hopefully

have a system in which lipids are well packed around the protein, while water

has not entered forbidden regions (Fig. 11 and Fig. 13). We will now proceed

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SanDisk Membrain Software Bedienungsanleitung Seite 41