Using the implicit membrane model IMM1

GMIN can now incorporate the IMM1 implicit membrane model described by <ref>Themis Lazaridis</ref>. To use this, first update and compile charmm and GMIN as described by Compiling_GMIN_with_CHARMM.

Previously Existing Terms

Since the use of a membrane introduces directionality to the system, previous parameters specifying orientation and spacial position become important. The system is optimised with respected to rotation, and the parameters behind the basin-hopping can be defined in the data file using the terms:

CHRIGIDROT prot rotmax nrot

This optimises rigid body rotation every nrot basin-hopping steps with maximum allowed probability prot and maximum allowed rotation angle rotmax (in degrees). Note that if including these terms in the data file, the directory must also contain a file entitled segment.tomove which specifies the segments for rotation. If 2 segments were to be rotated eg in a dimer, the segments.tomove files would be:

1
2

New Terms in GMIN

Two new terms have been included for use with the implicit membrane.

Firstly, the coordinates of the centre of mass of the system before the initial quench can be specified using:

SETCENTRE x y z

Specifying x y z as 0.0, 0.0, 0.0 will set the centre of mass at the origin and hence the centre of the membrane. A protein can be moved out of the membrane by altering the z coordinate.

Secondly, the system can be translated so that the centre-of-mass lies at the origin after every quench, using the keyword CENTRE. At present, CENTRE causes convergence issues as moving back to z=0 actually changes the energy. It is advised that CENTREXY is used instead, moving the protein back to (0,0,z) i.e. preserving the z-coordinate, by using the keyword:

CENTREXY

This solves the convergence problem mentioned above when using CENTRE.

CHARMM keywords

The charmm keywords are as follows:

eef1 setup membrane slvt water slv2 chex nsmth 10 width 26.0 temp 298.15 -
unit 93 name "/home/jwll2/svn/CHARMM31/toppar/solvpar.1.inp" aemp 0.85
!gouy anfr 0.3 area 70. conc 0.1 offset 3.0 valence 1
update ctonnb 7. ctofnb 9. cutnb 15. group rdie

The width of the membrane can be altered by altering the value 26.0. This refers to the width of the membrane in angstroms.

Uncommenting the commented line and adding a continuation to the line above allows the inclusion of Gouy Chapman theory adjustments to the membrane. This describes the effect of a static surface charge on the membrane potential.

Visualising the Membrane in VMD

VMD can be loaded using the command:

module load vmd/1.8.6

To view the membrane in VMD, first create a file called centre.pdb, with the following line of text:

ATOM      1  Ne      1      0.0  0.0  0.0  1.00  0.00      MAIN

This is simply an Ne atom placed at the origin. Also, obtain plotBox.tcl from clust:/sharedscratch/csw34/test/newcentre.

Load VMD and any molecules that you wish to visualise, followed by centre.pdb. Then open up the TK console and type:

source <PATH>/plotBox.tcl
plotBox z 30.0 30.0 13.0 0.0

The syntax of this: z refers to the direction of the surface normal of the membrane. 30.0 and 30.0 specify half the length of the membrane in the x and y directions in angstroms and can be increased if necessary. 13.0 describes half of the width of the membrane and 0.0 refers to the separation of the slab layers.

N.B It is important to load centre and input the commands into the console after all the molecules have been loaded. Otherwise the width of the membrane will be scaled by VMD.

NOTES

<references/>