SanDisk Membrain Software Manual do Utilizador descarregar pdf (Página 43)

3 RUNNING A SIMULATION OF KCSA 43

3.4 Production Runs

Now that the protein has been equilibrated, we are ready to perform production

runs. There will be one main diﬀerence with the previous simulations you have

already performed.

1 Open the ﬁle kcsa popcwieq-04.conf in a text e ditor.

2 Locate the sec tion # Constant Pressure Control. Note that we have

set the useConstantArea command to yes.

Simulation of membrane bilayers have shown that the c urrent CHARMM force-

ﬁeld parameters do no reproduce the expe rimentally observed area per lipid over

long MD trajectories. During the previous simulation steps, we let the are in

the xy-plane ﬂuctuate to permit packing of lipids against the protein. However,

after good packing has been observed, one should keep the area in the xy-plane

constant. Ideally, one should also compute the eﬀective area per lipid in the

system by computing the area of the simulations cell and subtracting from it

the protein area.

3 Run your simulation as indicated ab ove.

4 Look at the trajectory with VMD by loading PSF and corresponding dcd

ﬁles.

Production runs may feature additional parameters or employ diﬀerent com-

putational techniques that suit the purpose of the investigation being carried

out. The outcome of the simple production run presented here can already be

analyzed in a number of diﬀerent ways. For instance, you may want to try dif-

ferent VMD tools that allow you to compute density of water molecules, ions,

or lipids, as well as electrostatic p otentials, RMSD, motion of center of mass

and diﬀusion of molecules.

Final Homework. Set up a simulation of the Sodium Fo-ATP syn-

thase in POPC. The pdb code of the protein is 1YCE. Use only one

C11 ring (there are four in the pdb database), use DOWSER, and

place four lipid molecules inside of the ring (two on each side).

This ends the Membrane Proteins tutorial. We hope that you learned a lot

with it, and that you will make a great use of all the c apabilities VMD and

NAMD have to oﬀer for simulations of membrane protein systems.

Acknowledgements

Development of this tutorial was supported by the National Institutes of Health

(P41-RR005969 - Resource for Macromolecular Modeling and Bioinformatics).

1 2 ... 38 39 40 41 42 43

Sem comentários

SanDisk Membrain Software Manual do Utilizador Página 43