SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 35)

3 RUNNING A SIMULATION OF KCSA 35

NBFIX. The standard parameters for ions have been optimized to

reproduce bulk properties of ionic solutions, while the NBFIX pa-

rameters were optimized for the speciﬁc case of ions interacting

with carbonyl oxygen atoms as determined by Sergei Noskov, Si-

mon Bern`eche and Benoˆıt Roux, Nature 431, 830-834 2004.

6 Close the text editor with the parameter ﬁle and go back to the editor

with the NAMD conﬁguration ﬁle.

7 Locate the section labeled # Periodic Boundary Conditions. It should

look like:

# Periodic Boundary Conditions

# NOTE: Do not set the periodic cell basis if you have also

# specified an .xsc restart file!

if {1} {

cellBasisVector1 77. 0. 0.

cellBasisVector2 0. 77. 0.

cellBasisVector3 0. 0. 90.

cellOrigin 0.285711854696 0.299352765083 6.22171497345

}

wrapWater on

wrapAll on

We will check with VMD that the size and center of the system are correct.

8 Open VMD and load the ﬁles ../02-MEMBRANE/kcsa popcwi.psf and

../02-MEMBRANE/kcsa popcwi.pdb. Make sure you load the PDB ﬁle

into the PSF ﬁle.

9 Open the Tk Console window and type:

set all [atomselect top all]

measure center $all

measure minmax $all

The position of the center of the cell should roughly match the position found

in the NAMD conﬁguration ﬁle. However, the measure minmax command will

return values equivalent to cell dimensions that are larger than what we actually

have in the conﬁguration ﬁle ({84, 81, 90} instead of {77, 77, 90}). This apparent

inconsistency is caused by fragments of lipid molecules, which usually stick out

from the boundary of the simulation cell, but are not wrapped unless the center

of mass of the whole lipid crosses the periodic boundary. One can avoid this

problem by using a selection that does not contain lipids.

1 2 ... 30 31 32 33 34 35 36 37 38 39 40 41 42 43

Sem comentários

SanDisk Membrain Software Manual do Utilizador Página 35