SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 38)

3 RUNNING A SIMULATION OF KCSA 38

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

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

set all [atomselect top "all"]

$all set beta 0

set fixed [atomselect top "water or name CLA POT or protein or \

(chain L and name O2 P1 O3 O4 O1 C15 H52 H51 H11 C11 H12 \

N C14 H42 H43 H41 C12 H22 H23 H21 C13 H33 H31 H32)"]

$fixed set beta 1

$all writepdb kcsa popcwi.fix

exit

The commands you typed above created a ﬁle, kcsa popcwi.fix, that contains

zeros in the Beta ﬁeld of all lipid tails atoms, and ones in the Beta ﬁeld of all

other atoms.

Figure 12: Melting lipid tails

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

cept the command line

namd2 kcsa popcwimineq-01.conf > kcsa popcwimineq-01.log

in a terminal window. Check your local installation of NAMD and run it

accordingly.

Running. The solvated system containing KcsA embedded in a

membrane comprises over 40,000 atoms. Unless you have access

to a parallel computer with 10 or more nodes, we suggest that you

look at the trajectories provided in the example-output directory.

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SanDisk Membrain Software Manual do Utilizador Página 38