Using GMIN to generate endpoints (CHARMM) - Revision history

import>Csw34 at 14:54, 8 February 2012

2012-02-08T14:54:13Z

← Older revision		Revision as of 14:54, 8 February 2012
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	If you'd like to make sure that you have done this part right, you can find a complete set of output files		If you'd like to make sure that you have done this part right, you can find a complete set of output files
	[http://www-wales.ch.cam.ac.uk/chris/~~COPTIM_tutorial~~/metenk_CGMIN.tar.bz here].		[http://www-wales.ch.cam.ac.uk/chris/metenk_tutorial/metenk_CGMIN.tar.bz here].

	Now that we have a set of low energy minima, and a high energy extended structure, we can use [[OPTIM]] to connect them with pathways.		Now that we have a set of low energy minima, and a high energy extended structure, we can use [[OPTIM]] to connect them with pathways.

import>Csw34: /* Setting up CGMIN */

2012-02-08T13:50:48Z

Setting up CGMIN

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	STEP 80.0 0.0		STEP 80.0 0.0
	SAVE 10		SAVE 10
			CENTRE
	CHPMAX 0.4		CHPMAX 0.4
	CHPMIN 0.2		CHPMIN 0.2

import>Csw34: /* Setting up CGMIN */

2012-02-08T11:53:26Z

Setting up CGMIN

← Older revision		Revision as of 11:53, 8 February 2012
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	As before, you may need to make some changes to this file, so that the paths point correctly to your CHARMM files. If you are working in CUC3 in Cambridge, this may just be as simple as changing my CRSID (csw34) for yours.		As before, you may need to make some changes to this file, so that the paths point correctly to your CHARMM files. If you are working in CUC3 in Cambridge, this may just be as simple as changing my CRSID (csw34) for yours.

	Everything above the ''CHARMM'' line is a [[GMIN]] keyword. It is '''highly''' recommended that you take a look at the [[GMIN]] documentation [http://www-wales.ch.cam.ac.uk/GMIN.doc/node6.html here], so that you know what each of them does. In brief, we are doing up to 300 basin-hopping steps (or until the TARGET - the global minimum - is found), and at each step generating new coordinates by changing between - and 10 dihedral angles (backbone or sidechain) by up to 80 degrees.		Everything above the ''CHARMM'' line is a [[GMIN]] keyword. It is '''highly''' recommended that you take a look at the [[GMIN]] documentation [http://www-wales.ch.cam.ac.uk/GMIN.doc/node6.html here], so that you know what each of them does. In brief, we are doing up to 300 basin-hopping steps (or until the TARGET - the global minimum - is found), and at each step generating new coordinates by changing between 0 and 10 dihedral angles (backbone or sidechain) by up to 80 degrees.

	Everything below the ''CHARMM'' line is the CHARMM input that we use to set up the potential. If you'd like to know what this is doing, consult the CHARMM documentation! You may notice that is is very similar to the input we used to generate the ''metenk.crd'' file in the previous part of this tutorial.		Everything below the ''CHARMM'' line is the CHARMM input that we use to set up the potential. If you'd like to know what this is doing, consult the CHARMM documentation! You may notice that is is very similar to the input we used to generate the ''metenk.crd'' file in the previous part of this tutorial.

import>Csw34: /* Setting up CGMIN */

2012-02-08T11:52:31Z

Setting up CGMIN

← Older revision		Revision as of 11:52, 8 February 2012
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	<pre>		<pre>
	mkdir CGMIN		mkdir CGMIN
	cp metenk.~~pdb~~ CGMIN/input.crd		cp metenk.crd CGMIN/input.crd
			cd CGMIN
	</pre>		</pre>

import>Csw34: /* Running CGMIN */

2012-02-07T18:13:24Z

Running CGMIN

← Older revision		Revision as of 18:13, 7 February 2012
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	</pre>		</pre>
	This will load both sets of coordinates into a single molecule, that you can change between using the slider as if it was a trajectory. Frame 0 is the initial structure (initialmin.pdb) and frame 1 is the global minimum. You should see quite a difference!		This will load both sets of coordinates into a single molecule, that you can change between using the slider as if it was a trajectory. Frame 0 is the initial structure (initialmin.pdb) and frame 1 is the global minimum. You should see quite a difference!

			'''NOTE: if you are working on a cluster, you might need to load the vmd module first using:'''
			<pre>
			module load vmd
			</pre>

	If you'd like to make sure that you have done this part right, you can find a complete set of output files		If you'd like to make sure that you have done this part right, you can find a complete set of output files

import>Csw34: /* Running CGMIN */

2012-02-07T18:12:41Z

Running CGMIN

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	<pre>		<pre>
	vmd -pdb initialmin.pdb -pdb dbase.1.pdb		vmd -pdb initialmin.pdb -pdb dbase.1.pdb
	<pre>		</pre>
	This will load both sets of coordinates into a single molecule, that you can change between using the slider as if it was a trajectory. Frame 0 is the initial structure (initialmin.pdb) and frame 1 is the global minimum. You should see quite a difference!		This will load both sets of coordinates into a single molecule, that you can change between using the slider as if it was a trajectory. Frame 0 is the initial structure (initialmin.pdb) and frame 1 is the global minimum. You should see quite a difference!

import>Csw34: /* Running CGMIN */

2012-02-07T18:12:29Z

Running CGMIN

@@ Line 85: / Line 85: @@
 '''GMIN_out'''
 This is the primary GMIN output file, containing the energies of the minima found after each basin-hopping step, as well as the final 10 that have been saved in the ''dbase.x'' and ''dbase.x.pdb'' files. For example,
 <pre>
@@ Line 95: / Line 96: @@
 This line shows the final quench (tight convergence) for the lowest energy minimum found, in this case - it is the global minimum. We know this from previous work, which is why we added the TARGET line to the ''data' file. The coordinates of this minimum are saved in ''dbase.1'' in CHARMM .crd (CARD) format, and ''dbase.1.pdb'' in PDB format.
-==== dbase.x and dbase.x.pdb ====
+'''dbase.x and dbase.x.pdb'''

import>Csw34: /* GMIN_out */

2012-02-07T18:02:29Z

GMIN_out

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	This should take about a minute to run, it's pretty quick! Once it is done, you should have quite a few output files in the directory. There are a few important ones you might want to take a look at:		This should take about a minute to run, it's pretty quick! Once it is done, you should have quite a few output files in the directory. There are a few important ones you might want to take a look at:

	~~====~~ GMIN_out ~~====~~		'''GMIN_out'''
	This is the primary GMIN output file, containing the energies of the minima found after each basin-hopping step, as well as the final 10 that have been saved in the ''dbase.x'' and ''dbase.x.pdb'' files. For example,		This is the primary GMIN output file, containing the energies of the minima found after each basin-hopping step, as well as the final 10 that have been saved in the ''dbase.x'' and ''dbase.x.pdb'' files. For example,
	<pre>		<pre>
Line 93:		Line 93:
	Final Quench 1 energy= -157.0823478413 steps= 96 RMS force= 0.0000085 time= 28.85		Final Quench 1 energy= -157.0823478413 steps= 96 RMS force= 0.0000085 time= 28.85
	</pre>		</pre>
	This line shows the final quench (tight convergence) for the lowest energy minimum found, in this case - it is the global minimum. We know this from previous work, which is why we added the TARGET line to the ''data' file. The coordinates of this minimum are saved in ''dbase.1'' in CHARMM .crd (CARD) format, and ''dbase.1.pdb'' in PDB format.		This line shows the final quench (tight convergence) for the lowest energy minimum found, in this case - it is the global minimum. We know this from previous work, which is why we added the TARGET line to the ''data' file. The coordinates of this minimum are saved in ''dbase.1'' in CHARMM .crd (CARD) format, and ''dbase.1.pdb'' in PDB format.

	==== dbase.x and dbase.x.pdb ====		==== dbase.x and dbase.x.pdb ====

import>Csw34 at 18:02, 7 February 2012

2012-02-07T18:02:03Z

← Older revision		Revision as of 18:02, 7 February 2012
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	CGMIN > charmm.out &		CGMIN > charmm.out &
	</pre>		</pre>

			This should take about a minute to run, it's pretty quick! Once it is done, you should have quite a few output files in the directory. There are a few important ones you might want to take a look at:

			==== GMIN_out ====
			This is the primary GMIN output file, containing the energies of the minima found after each basin-hopping step, as well as the final 10 that have been saved in the ''dbase.x'' and ''dbase.x.pdb'' files. For example,
			<pre>
			Qu 2 E= -144.0873506553 steps= 518 RMS= 0.90078E-03 Markov E= -143.4215906 t= 0.5
			</pre>
			This is the line summarising the result of the second 'quench' (basin-hopping step). The energy of the minimum found after 518 L-BFGS minimisation steps is -144.0873506553, which is them compared to the current markov energy of -143.4215906. As this energy is lower, this minimum will replace the current markov minimum, and the next step will start from this conformation.
			<pre>
			Final Quench 1 energy= -157.0823478413 steps= 96 RMS force= 0.0000085 time= 28.85
			</pre>
			This line shows the final quench (tight convergence) for the lowest energy minimum found, in this case - it is the global minimum. We know this from previous work, which is why we added the TARGET line to the ''data' file. The coordinates of this minimum are saved in ''dbase.1'' in CHARMM .crd (CARD) format, and ''dbase.1.pdb'' in PDB format.

			==== dbase.x and dbase.x.pdb ====

import>Csw34 at 17:50, 7 February 2012

2012-02-07T17:50:01Z

← Older revision		Revision as of 17:50, 7 February 2012
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	We can use [[GMIN]] to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using [[OPTIM]] to form a pathway. After that, we can use [[PATHSAMPLE]] to calculate the rate of interconversion of these endpoints, taking into account multiple pathways.		We can use [[GMIN]] to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using [[OPTIM]] to form a pathway. After that, we can use [[PATHSAMPLE]] to calculate the rate of interconversion of these endpoints, taking into account multiple pathways.

	=== Setting up ~~for~~ CGMIN ===		=== Setting up CGMIN ===
	Copy the ''metenk.crd'' file you have just created into a new directory, and rename it ''input.crd''. CGMIN expects the input to always be called 'input.crd'.		Copy the ''metenk.crd'' file you have just created into a new directory, and rename it ''input.crd''. CGMIN expects the input to always be called 'input.crd'.
	<pre>		<pre>