SanDisk Membrain Software Bedienungsanleitung PDF herunterladen (Seite 40)

3 RUNNING A SIMULATION OF KCSA 40

5 Check that the line “temperature $temperature” has been commented

out (with a #).

Now that velocities (which determine temperature) have been read from the

previous run, we do not need to set the initial temperature here. Note also that

information about the periodic cell is also read from a restart ﬁle, and therefore

the # Periodic Boundary Conditions section has been deactivated.

6 Because we will no longer ﬁx atoms in the system, check that the # Fixed

Atoms Constraint section has been deactivated as well.

7 Locate the section labeled ## EXTRA PARAMETERS. There are two addi-

tional s ets of parameters in this section:

constraints on

consexp 2

consref kcsa_popcwi.pdb

conskfile kcsa_popcwin.cnst

conskcol B

margin 3

tclforces on

set waterCheckFreq 100

set lipidCheckFreq 100

set allatompdb ../02-MEMBRANE/kcsa_popcwi.pdb

tclForcesScript keep_water_out.tcl

The ﬁrst set of additional parameters impose harmonic constraints on the pro-

tein. Harmonics constraints are applied using a PDB ﬁle that tags the atoms to

be restrained. This ﬁle will be generated below. The use of such harmonic con-

straints permits lipids, water, and ions to adapt to the protein in its crystal form.

In addition, we use the margin 3 command to allow large volume ﬂuctuations

that are typical during the ﬁrst dynamics of a new system in an NpT ensem-

ble. Otherwise, the simulation will likely ﬁnish with the message: FATAL ERROR:

Periodic cell has become too small for original patch grid! (in which

case you should just restart your simulation from the las t saved restart ﬁles).

The second set of additional parameters calls a Tcl script, named

keep water out.tcl, which prevents hydration of the membrane-protein inter-

face during equilibration.

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SanDisk Membrain Software Bedienungsanleitung Seite 40