Difference between revisions of "Using the implicit membrane model IMM1"
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| + | Must mention the terms that charmm reads ie width etc |
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[[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 Themis Lazaridis (1). To use this, first update and compile charmm and GMIN as described by [[Compiling_GMIN_with_CHARMM]]. |
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===New Terms in GMIN=== |
===New Terms in GMIN=== |
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| − | Two new terms have been included for use with the implicit membrane. |
+ | Two new terms have been included for use with the implicit membrane. |
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| + | Firstly, the coordinates of the centre of mass of the system before the initial quench can be specified using: |
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<pre> |
<pre> |
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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. |
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| − | Secondly, |
+ | Secondly, the protein can be moved back to (0,0,z) i.e. the z-coordinate preserved by using the keyword: |
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| + | CENTREXY |
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| + | This solves the convergence problem mentioned above when using CENTRE. |
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| + | ===Visualising the Membrane in VMD=== |
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| + | VMD can be loaded using the command: |
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| − | ------------------------------------------------------------------------------------- |
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| − | A shorter dump interval is recommended as system size (and therefore time/quench) increases. To restore a run, you need the '''RESTORE''' keyword. Here are two excerpts from example data files to demonstrate: |
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| − | Original data file: |
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<pre> |
<pre> |
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| + | module load vmd/1.8.6 |
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| − | ... |
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| − | DUMPINT 100 |
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| − | STEPS 10000 |
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| − | SAVE 100 |
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| − | ... |
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</pre> |
</pre> |
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| + | 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. |
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| − | data file for restarted run: |
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| − | ... |
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| − | DUMPINT 100 |
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| − | RESTORE GMIN.dump |
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| − | STEPS 15000 |
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| − | SAVE 100 |
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| − | ... |
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| + | 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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| − | The number of steps in the new data file should always be greater than in the original. In this case, the run is being restarted for a further 5000 quenches - 10000 + 5000 = 15000! The [[makerestart]] script does a lot of this for you. |
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| − | ===What if I want to change the value of SAVE?=== |
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| − | For large systems, it is nice to have the flexibility to change the number of structures that are tightly converged and dumped at the end of a run. This is because final quenches often take a long time, and you may only need to see one or two structures at the start of a long series of restart runs. If your dump file was generated by a version of [[GMIN]] compiled from the repository after 30/9/2008, you can do this by simply changing the value of '''SAVE''' in the new data file. If not, you need to make a simple modification to the dump file before you use it. Open the dump file in an editor e.g. vi: |
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<pre> |
<pre> |
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| + | source <PATH>/plotBox.tcl |
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| − | vi GMIN.dump |
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| + | plotBox z 30.0 30.0 13.0 0.0 |
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| − | </pre> |
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| − | In the new format, there is an extra line in the dump file which details the number of structures saved in the previous run. You need to input this manually if you have an old dump file, otherwise it will not be read in correctly. Here is an example, first the original - old dump file: |
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| − | <pre> |
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| − | steps completed J1 in mc |
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| − | 13000 |
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| − | COORDS |
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| − | run number 1 |
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| − | 22.174000000000000 83.915460000000000 47.511220000000000 |
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| − | 21.352510000000000 82.452780000000000 47.773840000000000 |
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| − | 22.240000000000000 82.880000000000000 47.440000000000000 |
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| − | ... |
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</pre> |
</pre> |
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| + | 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. |
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| − | Here, 13000 quenches have been done. Looking at the old data file above - we know that 100 structures were saved. This info must now be included in the dump file. The modification is performed as follows: |
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| − | <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. |
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| − | steps completed J1 in mc |
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| − | 13000 |
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| − | 100 |
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| − | COORDS |
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| − | run number 1 |
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| − | 22.174000000000000 83.915460000000000 47.511220000000000 |
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| − | 21.352510000000000 82.452780000000000 47.773840000000000 |
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| − | 22.240000000000000 82.880000000000000 47.440000000000000 |
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| − | ... |
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| − | </pre> |
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| − | With this change done, you are now free to set '''SAVE''' to anything you'd like for the restart run. |
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Revision as of 13:51, 17 July 2009
Must mention the terms that charmm reads ie width etc
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.
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:
CHPMAX 0.4 CHPMIN 0.2 CHNMAX 10 CHNMIN 0
These parameters are described in the GMIN documentation. Note that if including these terms in the data file, the directory must also contain a file entitled segment.tomove which contains the single character:
1
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 data file the term:
CENTRE
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).
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 <i>x</i> <i>y</i> <i>z</i>
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 protein can be moved back to (0,0,z) i.e. the z-coordinate preserved by using the keyword:
CENTREXY
This solves the convergence problem mentioned above when using CENTRE.
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 obtain the files centre.pdb and plotBox.tcl. These can be found at 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.