SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 42)

3 RUNNING A SIMULATION OF KCSA 42

Figure 13: Achieving a good packing of lipids around the protein. Note the

gaps in the membrane–protein interface (left panel) before proper equilibration

(right panel).

to release the harmonic constraints and further equilibrate the whole system.

1 Open the ﬁle kcsa popcwieq-03.conf in a text e ditor.

2 Locate the section labeled # Continuing a job from the restart files

and note how we use the output ﬁles of our previous run to set starting

coordinates, velocities, and simulation cell size.

3 Go to the ## EXTRA PARAMETERS section and check that the restraints

are actually not there. The Tcl script keep water out.tcl is also not

called this time. The command margin is eliminated as well, because

large volume ﬂuctuations are not expected after the initial equilibration.

4 Look at the end of the conﬁguration ﬁle. We have eliminated the mini-

mization step in the present simulation.

5 Run your simulation as indicated above, using now the NAMD conﬁgura-

tion ﬁle kcsa popcwieq-03.conf.

After the simulation is done, your system should be equilibrated fairly well. You

can monitor the stability of the protein through the computation of RMSDs and

by looking at the resulting trajectory with VMD.

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SanDisk Membrain Software Manual do Utilizador Página 42