Using the implicit membrane model IMM1 - Revision history

import>Jwll2 at 13:12, 22 July 2009

2009-07-22T13:12:51Z

← Older revision		Revision as of 13:12, 22 July 2009
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	<b>membrane</b> introduces the membrane model and <b>slvt water</b> and <b>slv2 chex</b> specify that the exterior solvent is water and that the interior solvent is cyclohexane. <b>nsmith</b>, set to 10 as a default, determines how steep the transition is at the interface between interior and exterior. The <b>width</b> of the membrane can be altered by altering the value 26.0. This refers to the width of the membrane in angstroms and usually has a value 25-30. The last keyword <b>aemp</b>, default 0.85, determines the extent of strengthening of electrostatic interactions in the membrane (the smaller, the stronger). This parameter was empirically adjusted to give reasonable membrane insertion energies for model systems.		<b>membrane</b> introduces the membrane model and <b>slvt water</b> and <b>slv2 chex</b> specify that the exterior solvent is water and that the interior solvent is cyclohexane. <b>nsmith</b>, set to 10 as a default, determines how steep the transition is at the interface between interior and exterior. The <b>width</b> of the membrane can be altered by altering the value 26.0. This refers to the width of the membrane in angstroms and usually has a value 25-30. The last keyword <b>aemp</b>, default 0.85, determines the extent of strengthening of electrostatic interactions in the membrane (the smaller, the stronger). This parameter was empirically adjusted to give reasonable membrane insertion energies for model systems.

	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. <b>anfr</b> describes the molar fraction of anionic lipids (e.g. a 70/30 mixture of PC/PG corresponds to ANFR 0.3, which is the default). <b>area<b> is the area (Angstrom^2) per lipid (default 70) and <b>offset<b> is the distance of the plane of negative charge, usually the phosphates, from the hydrocarbon/water boundary (default 3). <b>conc</b> and <b>valence</b> is the molarity and valence of the salt (default 0.1 and 1, respectively).		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. <b>anfr</b> describes the molar fraction of anionic lipids (e.g. a 70/30 mixture of PC/PG corresponds to ANFR 0.3, which is the default). <b>area</b> is the area (Angstrom^2) per lipid (default 70) and <b>offset</b> is the distance of the plane of negative charge, usually the phosphates, from the hydrocarbon/water boundary (default 3). <b>conc</b> and <b>valence</b> is the molarity and valence of the salt (default 0.1 and 1, respectively).

import>Jwll2 at 21:20, 21 July 2009

2009-07-21T21:20:58Z

← Older revision		Revision as of 21:20, 21 July 2009
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	[[GMIN]] can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis. To use this, first update and compile charmm and GMIN as described by [[Compiling_GMIN_with_CHARMM]].		[[GMIN]] can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis [http://www3.interscience.wiley.com/cgi-bin/fulltext/104537101/HTMLSTART]. To use this, first update and compile charmm and GMIN as described by [[Compiling_GMIN_with_CHARMM]].

	===Previously Existing Terms===		===Previously Existing Terms===
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	N.B It is important to load centre and input the commands into the console <i>after</i> all the molecules have been loaded. Otherwise the width of the membrane will be scaled by VMD.		N.B It is important to load centre and input the commands into the console <i>after</i> all the molecules have been loaded. Otherwise the width of the membrane will be scaled by VMD.

	===References===

	T. Lazaridis, Proteins, 52:176-92, 2003

	Birgit Strodel for the keyword parameters

import>Jwll2 at 21:14, 21 July 2009

2009-07-21T21:14:00Z

← Older revision		Revision as of 21:14, 21 July 2009
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	</pre>		</pre>

	This is simply an Ne atom placed at the origin. Also, obtain <i>plotBox.tcl</i> from ~~clust~~:/~~sharedscratch~~/~~csw34~~/~~test~~/~~newcentre~~.		This is simply an Ne atom placed at the origin. Also, obtain <i>plotBox.tcl</i> from the Wales Group homepage [http://www-wales.ch.cam.ac.uk/~wales/plotBox.tcl].

	Load VMD and any molecules that you wish to visualise, followed by <i>centre.pdb</i>. Then open up the TK console and type:		Load VMD and any molecules that you wish to visualise, followed by <i>centre.pdb</i>. Then open up the TK console and type:
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	T. Lazaridis, Proteins, 52:176-92, 2003		T. Lazaridis, Proteins, 52:176-92, 2003

	Birgit Strodel for the keyword parameters		Birgit Strodel for the keyword parameters

import>Jwll2 at 18:33, 21 July 2009

2009-07-21T18:33:18Z

← Older revision		Revision as of 18:33, 21 July 2009
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	</pre>		</pre>

			<b>membrane</b> introduces the membrane model and <b>slvt water</b> and <b>slv2 chex</b> specify that the exterior solvent is water and that the interior solvent is cyclohexane. <b>nsmith</b>, set to 10 as a default, determines how steep the transition is at the interface between interior and exterior. The <b>width</b> of the membrane can be altered by altering the value 26.0. This refers to the width of the membrane in angstroms and usually has a value 25-30. The last keyword <b>aemp</b>, default 0.85, determines the extent of strengthening of electrostatic interactions in the membrane (the smaller, the stronger). This parameter was empirically adjusted to give reasonable membrane insertion energies for model systems.
	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. <b>anfr</b> describes the molar fraction of anionic lipids (e.g. a 70/30 mixture of PC/PG corresponds to ANFR 0.3, which is the default). <b>area<b> is the area (Angstrom^2) per lipid (default 70) and <b>offset<b> is the distance of the plane of negative charge, usually the phosphates, from the hydrocarbon/water boundary (default 3). <b>conc</b> and <b>valence</b> is the molarity and valence of the salt (default 0.1 and 1, respectively).

	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===		===Visualising the Membrane in VMD===
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	T. Lazaridis, Proteins, 52:176-92, 2003		T. Lazaridis, Proteins, 52:176-92, 2003
			Birgit Strodel for the keyword parameters

import>Jwll2 at 14:56, 21 July 2009

2009-07-21T14:56:19Z

← Older revision		Revision as of 14:56, 21 July 2009
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	[[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]].		[[GMIN]] can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis. To use this, first update and compile charmm and GMIN as described by [[Compiling_GMIN_with_CHARMM]].

	===Previously Existing Terms===		===Previously Existing Terms===
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	===CHARMM keywords===		===CHARMM keywords===

			The toppar parameters that should be used are the EEF1.1.inp files. This is done using:

			<pre>
			open read unit 11 card name toph19_eef1.1.inp
			read rtf card unit 11
			close unit 11

			open read unit 12 card name param19_eef1.1.inp
			read para card unit 12
			close unit 12
			</pre>

	The charmm keywords are as follows:		The charmm keywords are as follows:
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	N.B It is important to load centre and input the commands into the console <i>after</i> all the molecules have been loaded. Otherwise the width of the membrane will be scaled by VMD.		N.B It is important to load centre and input the commands into the console <i>after</i> all the molecules have been loaded. Otherwise the width of the membrane will be scaled by VMD.

	==~~NOTES~~==		===References===

			T. Lazaridis, Proteins, 52:176-92, 2003
	<references/>

import>Jwll2 at 14:46, 21 July 2009

2009-07-21T14:46:38Z

← Older revision		Revision as of 14:46, 21 July 2009
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	<pre>		<pre>
			CHRIGIDROT prot rotmax nrot
	CHPMAX 0.4
	CHPMIN 0.2
	CHNMAX 10
	CHNMIN 0
	</pre>		</pre>

	~~These~~ ~~parameters~~ ~~are~~ ~~described~~ in ~~the~~ ~~GMIN~~ ~~documentation~~. <b>Note that if including these terms in the <i>data</i> file, the directory must also contain a file entitled <i>segment.tomove</i> which ~~contains~~ the ~~single~~ ~~character~~:</b>		This optimises rigid body rotation every nrot basin-hopping steps with maximum allowed probability prot and maximum allowed rotation angle rotmax (in degrees). <b>Note that if including these terms in the <i>data</i> file, the directory must also contain a file entitled <i>segment.tomove</i> which specifies the segments for rotation. If 2 segments were to be rotated eg in a dimer, the segments.tomove files would be:</b>

	<pre>		<pre>
	1		1
			2
	</pre>		</pre>

	The system can be translated so that the centre-of-mass lies at the origin after every quench. This is achieved by including in the <i>data</i> file the term:

⚫	<pre>
	CENTRE
⚫	</pre>

	At present, CENTRE causes convergence issues as moving back to z=0 actually changes the energy. It is advised that CENTREXY is used instead (see below).

	===New Terms in GMIN===		===New Terms in GMIN===
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	Specifying <i>x</i> <i>y</i> <i>z</i> 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 <i>z</i> coordinate.		Specifying <i>x</i> <i>y</i> <i>z</i> 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 <i>z</i> coordinate.

	Secondly, the ~~protein~~ can be ~~moved~~ back to (0,0,z) i.e. the z-coordinate ~~preserved~~ by using the keyword:		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:

	<pre>		<pre>
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	<pre>		<pre>
	eef1 setup membrane slvt water slv2 chex nsmth 10 width 26.0 temp 298.15 -		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 -		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		!gouy anfr 0.3 area 70. conc 0.1 offset 3.0 valence 1
	update ctonnb 7. ctofnb 9. cutnb 15. group rdie		update ctonnb 7. ctofnb 9. cutnb 15. group rdie
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	The width of the membrane can be altered by altering the value 26.0. This refers to the width of the membrane in angstroms.		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 allows the inclusion of Gouy Chapman theory adjustments to the membrane. This describes the effect of a static surface charge on the membrane		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.
	potential.

	===Visualising the Membrane in VMD===		===Visualising the Membrane in VMD===
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	</pre>		</pre>


⚫	To ~~view~~ ~~the~~ ~~membrane~~ in ~~VMD,~~ ~~first~~ ~~obtain~~ the ~~files <i>centre~~.~~pdb</i>~~ ~~and~~ <i>plotBox.tcl</i>. ~~These can be found at~~ clust:/sharedscratch/csw34/test/newcentre.
			To view the membrane in VMD, first create a file called <i>centre.pdb</i>, with the following line of text:

		⚫	<pre>
			ATOM 1 Ne 1 0.0 0.0 0.0 1.00 0.00 MAIN
		⚫	</pre>

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

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

import>Jwll2 at 14:20, 17 July 2009

2009-07-17T14:20:58Z

← Older revision		Revision as of 14:20, 17 July 2009
Line 61:		Line 61:
	Uncommenting the commented line allows the inclusion of Gouy Chapman theory adjustments to the membrane. This describes the effect of a static surface charge on the membrane		Uncommenting the commented line allows the inclusion of Gouy Chapman theory adjustments to the membrane. This describes the effect of a static surface charge on the membrane
	potential.		potential.


	===Visualising the Membrane in VMD===		===Visualising the Membrane in VMD===

import>Jwll2 at 14:11, 17 July 2009

2009-07-17T14:11:33Z

← Older revision		Revision as of 14:11, 17 July 2009
Line 1:		Line 1:
	[[GMIN]] can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis ~~(1)~~. To use this, first update and compile charmm and GMIN as described by [[Compiling_GMIN_with_CHARMM]].		[[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 <i>data</i> file using the 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 <i>data</i> file using the terms:
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	<pre>		<pre>
	SETCENTRE ''x y z''		SETCENTRE x y z
	</pre>		</pre>

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

			==NOTES==

			<references/>

import>Jwll2 at 14:00, 17 July 2009

2009-07-17T14:00:26Z

← Older revision		Revision as of 14:00, 17 July 2009
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	</pre>		</pre>

	At present, CENTRE causes convergence issues as moving back to z=0 actually changes the energy. It is advised ~~the~~ CENTREXY is used instead (see below).		At present, CENTRE causes convergence issues as moving back to z=0 actually changes the energy. It is advised that CENTREXY is used instead (see below).

	===New Terms in GMIN===		===New Terms in GMIN===
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	<pre>		<pre>
	SETCENTRE ~~<i>~~x~~</i>~~ ~~<i>~~y~~</i>~~ ~~<i>~~z~~</i>~~		SETCENTRE ''x y z''
	</pre>		</pre>

import>Jwll2 at 13:56, 17 July 2009

2009-07-17T13:56:58Z

@@ Line 1: / Line 1: @@
 [[GMIN]] can now incorporate the IMM1 implicit membrane model described by Themis Lazaridis (1). To use this, first update and compile charmm and GMIN as described by [[Compiling_GMIN_with_CHARMM]].
@@ Line 45: / Line 43: @@
 This solves the convergence problem mentioned above when using CENTRE.
 ===Visualising the Membrane in VMD===
@@ Line 56: / Line 71: @@
 To view the membrane in VMD, first obtain the files <i>centre.pdb</i> and <i>plotBox.tcl</i>. These can be found at clust:/sharedscratch/csw34/test/newcentre.
-Load VMD and any molecules that you wish to visualise, followed by <i>centre.pdb<i>. Then open up the TK console and type:
+Load VMD and any molecules that you wish to visualise, followed by <i>centre.pdb</i>. Then open up the TK console and type:
 <pre>