SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 36)

3 RUNNING A SIMULATION OF KCSA 36

10 Type in the Tk Console:

set wat [atomselect top water]

measure minmax $wat

The output of measure minmax should now be consistent with the sim-

ulation c ell size speciﬁed in the NAMD conﬁguration ﬁle. It is always

desirable to give a bit of extra (∼ 1

A) space between the boundary atoms

of your system and the boundaries of the simulation cell.

11 Lets visually check our periodic cell dimensions. Type in the Tk C onsole:

molinfo top set a 77

molinfo top set b 77

molinfo top set c 90

12 Select the Graphics → Representations... menu item and then click on the

Periodic tab of the Graphical Representations window. Select diﬀerent

periodic images to draw and check that the gap between periodic images

is small or negligible (use also the cell dimensions obtained when using

the “all” selection and check the undesirable large gaps present between

periodic images in such a case, Fig. 11).

Figure 11: Setting up the right cell dimensions for periodic boundary conditions.

Left panel shows periodic arrangement with gaps (overestimated size of the

system). Center panel shows the same system but using a better estimate of

the simulation cell size. Right panel, periodic arrangement after se veral steps

of minimization and equilibration.

13 Close VMD and return to the text editor containing the NAMD conﬁgura-

tion ﬁle. Locate the section labeled #PME (for full-system periodic

electrostatics). It should look like:

#PME (for full-system periodic electrostatics)

if {1} {

PME yes

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SanDisk Membrain Software Manual do Utilizador Página 36