Loading OPTIM's min.data.info files into PATHSAMPLE - Revision history

import>Ss2029 at 14:28, 26 May 2011

2011-05-26T14:28:08Z

← Older revision		Revision as of 14:28, 26 May 2011
Line 71:		Line 71:
	Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files.		Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files.

	To do something useful lets compute the heat capacity as a function of temperature.		To do something useful lets compute the heat capacity as a function of temperature, based on the harmonic superposition approximation.

	1. Create two files min.A and min.B:		1. Create two files min.A and min.B:

2011-05-25T14:46:29Z

← Older revision		Revision as of 14:46, 25 May 2011
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	to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM).		to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM).

	3. Running PATHSAMPLE now should generate '''Cv.out''' with two columns - first ~~containing~~ temperature and second ~~with~~ heat capacity.		3. Running PATHSAMPLE now should generate '''Cv.out''' with two columns - first for temperature and second for heat capacity.

			--[[User:Ss2029\|Ss2029]] 14:46, 25 May 2011 (UTC)

2011-05-25T14:45:08Z

← Older revision		Revision as of 14:45, 25 May 2011
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	</pre>		</pre>

	2. In pathdata, comment out READMIN and add ~~line~~		2. In pathdata, comment out READMIN and add the CV command as

			<pre>
⚫	~~'''~~CV 0.1 1.0 0.01~~'''~~
			...
			comment READMIN min.data.info.initial
		⚫	CV 0.1 1.0 0.01
			...
			</pre>

	to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM).		to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM).

2011-05-25T14:44:16Z

← Older revision		Revision as of 14:44, 25 May 2011
Line 73:		Line 73:
	To do something useful lets compute the heat capacity as a function of temperature.		To do something useful lets compute the heat capacity as a function of temperature.

	Create two files min.A and min.B		1. Create two files min.A and min.B:

	<pre>		<pre>
Line 83:		Line 83:
	2		2
	</pre>		</pre>

			2. In pathdata, comment out READMIN and add line

			'''CV 0.1 1.0 0.01'''

			to compute Cv from T=0.1 to 1.0 in steps of 0.01 (unit = kcal/mol for AMBER and CHARMM).

			3. Running PATHSAMPLE now should generate '''Cv.out''' with two columns - first containing temperature and second with heat capacity.

2011-05-25T14:39:49Z

← Older revision		Revision as of 14:39, 25 May 2011
Line 70:		Line 70:

	Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files.		Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files.

			To do something useful lets compute the heat capacity as a function of temperature.

			Create two files min.A and min.B

			<pre>
			> more min.A
			1
			1
			> more min.B
			1
			2
			</pre>

2011-05-25T14:35:09Z

← Older revision		Revision as of 14:35, 25 May 2011
Line 69:		Line 69:
	</pre>		</pre>

	Running PATHSAMPLE now should generate '''points.min''' and '''min.data'''.		Running PATHSAMPLE now should generate '''points.min''' and '''min.data''', the final required files.

2011-05-25T14:33:49Z

← Older revision		Revision as of 14:33, 25 May 2011
Line 36:		Line 36:
	cat min.data.info.* > min.data.info.initial		cat min.data.info.* > min.data.info.initial
	</pre>		</pre>

			In a new directory copy the following files:
			<pre>
			coords.inpcrd, coords.prmtop, min.data.info.initial, perm.allow, pathdata
			</pre>

			Listing of pathdata

			<pre>
			DEBUG
			COPYFILES perm.allow min.in coords.inpcrd coords.prmtop
			CLOSEFILES
			NATOMS 22
			PERMDIST
			SYSTEM AMBER
			NAB
			CONNECTIONS 1
			SEED 1
			PERTURB 0.40
			ETOL 1.0D-7
			GEOMDIFFTOL 0.1
			ITOL 1.0D0
			DIRECTION AB
			EXEC /home/wales/bin/A9OPTIM
			TRIPLES
			ADDTRIPLES
			STARTTRIPLES
			CYCLES 0
			CPUS 1
			TEMPERATURE 0.59
			READMIN min.data.info.initial
			</pre>

			Running PATHSAMPLE now should generate '''points.min''' and '''min.data'''.

2011-05-25T14:22:18Z

@@ Line 2: / Line 2: @@
 <pre>
-WORK/GMIN/coord.1 to coord.N - N minima generated by GMIN
+coord.1 to coord.N - N minima generated by GMIN
++
 coords.inpcrd, coords.prmtop, perm.allow, min.in
@@ Line 21: / Line 21: @@
 NAB start
 POINTS
 </pre>

2011-05-25T14:15:59Z

← Older revision		Revision as of 14:15, 25 May 2011
Line 1:		Line 1:
	Input:		Input files:

	<pre>		<pre>
	WORK/GMIN/coord.1 to coord.N - N minima generated by GMIN		WORK/GMIN/coord.1 to coord.N - N minima generated by GMIN
	+		+
	coords.inpcrd, coords.prmtop, perm.allow, min.in		coords.inpcrd, coords.prmtop, perm.allow, min.in
	+		+
	odata, the optim input file		odata, the optim input file
			</pre>

			Listing of odata used with Amber OPTIM (exec A9OPTIM)
			<pre>
			DEBUG
			UPDATES 6000
			DUMPDATA
			ENDHESS
			MAXERISE 1.0D-4 1.0D0
			BFGSMIN 1.0D-6
			BFGSSTEPS 1000
			MAXBFGS 0.2
			NAB start
			POINTS
	</pre>		</pre>

2011-05-25T14:14:35Z

← Older revision		Revision as of 14:14, 25 May 2011
Line 1:		Line 1:
	Input:		Input:

			<pre>
	WORK/GMIN/coord.1 to coord.N - N minima generated by GMIN		WORK/GMIN/coord.1 to coord.N - N minima generated by GMIN

	+		+

	coords.inpcrd, coords.prmtop, perm.allow, min.in		coords.inpcrd, coords.prmtop, perm.allow, min.in

	+		+

	odata, the optim input file		odata, the optim input file
			</pre>