Global optimization of biomolecules using AMBER9 - Revision history

import>Khs26 at 15:43, 22 September 2009

2009-09-22T15:43:15Z

← Older revision		Revision as of 15:43, 22 September 2009
Line 32:		Line 32:
	ntpr = 500, ntwx = 500, ntwr=500,		ntpr = 500, ntwx = 500, ntwr=500,
	nrespa=1,		nrespa=1,
	cut = 8.22,		cut = 999.0,
	rgbmax = 8.22,		rgbmax = 8.22,
	ifswitch = 1,		ifswitch = 1,
Line 44:		Line 44:
	<b>saltcon=0.2</b> sets the surrounding (monovalent) salt concentration to 0.2 [mol/L].		<b>saltcon=0.2</b> sets the surrounding (monovalent) salt concentration to 0.2 [mol/L].

	<b>~~temp1~~ = 0</b> sets the initial ~~tempe~~ <b>temp0 = ~~700~~</b> sets final temperature in Kelvin.		<b>tempi = 0</b> sets the initial temperature <b>temp0 = 400</b> sets final temperature in Kelvin.

	.5ps of MD with a 1.0fs time step is set by<b>nstlim=500, dt=0.001</b>		.5ps of MD with a 1.0fs time step is set by<b>nstlim=500, dt=0.001</b>

	<b> ntt=3 </b> Langevin dynamics with <b> gamma_ln = 1.0 </b> sets frequency of coupling to heat bath to the collision rate of 1 ps-1		<b> ntt=3 </b> Langevin dynamics with <b> gamma_ln = 10.0 </b> sets frequency of coupling to heat bath to the collision rate of 10 ps-1

	<b>ntpr = 100 </b> Energy output frequency		<b>ntpr = 100 </b> Energy output frequency

2009-09-11T12:35:42Z

@@ Line 36: / Line 36: @@
       ifswitch = 1,
+   /
 . ''data'' -- file with GMIN keywords:
-   SLOPPYCONV 1.0D-6
+  SLOPPYCONV   1.0D-2
-   TIGHTCONV  1.0D-7
+  TIGHTCONV    1.0D-3
-   MAXIT      100 600
+  MAXERISE     0.001
-   MAXBFGS    1.0
+  STEPS        100  1.0
-   SAVE       100
+  STEP         0.00 0.0
-   STEP       0.0
+  AMBERMDSTEPS
 Thats all for the beginning!

2009-09-11T12:28:23Z

← Older revision		Revision as of 12:28, 11 September 2009
Line 7:		Line 7:
	3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculates only energy of the system, e.g.:		3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculates only energy of the system, e.g.:

	Minimization		# Minimization Parameters
	&cntrl		&cntrl
	imin~~=1,~~ ~~maxcyc=1,~~ ~~ncyc~~=1,		imin = 1,
	~~igb=2,~~ ~~saltcon~~=~~0.2~~,		ncyc = 1,
	~~ntx=1,~~ ~~ntb~~=0,		maxcyc = 1,
	~~cut~~=~~999.~~0		igb = 2, saltcon=0.1,
		⚫	ntb = 0,
⚫	/
			cut = 8.22,
			rgbmax = 8.22,
			ifswitch = 1,
		⚫	/

	4. ''min_md.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.:		4. ''min_md.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.:

			# MD Paramaters
	STOP
	&cntrl		&cntrl
	imin = 0,		imin = 0,
	tempi = ~~500~~.0, temp0 = ~~700~~.0,		tempi = 0.0, temp0 = 400.0,
	ntt = 3, gamma_ln = 1.0,		ntt = 3, gamma_ln = 10.0,
	nstlim = ~~300~~, dt = 0.001,		nstlim = 500, dt = 0.001,
	igb = 2, saltcon = 0.2,		igb = 2, saltcon = 0.1,
	ntb = 0,		ntb = 0,nscm=0,
	~~ntpr~~ = ~~100~~, ~~ntwx~~ = ~~100~~, ~~nrespa=1,~~		ntc = 2,ntf = 2,
			ntpr = 500, ntwx = 500, ntwr=500,
⚫	~~cut~~ = ~~999.~~0
			nrespa=1,
			cut = 8.22,
			rgbmax = 8.22,
			ifswitch = 1,
	/		/

2008-05-30T15:27:45Z

← Older revision		Revision as of 15:27, 30 May 2008
Line 15:		Line 15:
	/		/

	4. ''~~min_cd~~.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.:		4. ''min_md.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.:

	STOP		STOP

2008-05-01T17:55:50Z

← Older revision		Revision as of 17:55, 1 May 2008
Line 5:		Line 5:
	2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])		2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])

	3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 ~~calculated~~ only energy of the system, e.g.:		3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculates only energy of the system, e.g.:

	Minimization		Minimization

2008-05-01T17:55:33Z

← Older revision		Revision as of 17:55, 1 May 2008
Line 5:		Line 5:
	2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])		2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])

	3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, ~~for~~ ~~one~~ ~~cycle~~ only), e.g.:		3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculated only energy of the system, e.g.:

	Minimization		Minimization

2008-05-01T10:39:42Z

← Older revision		Revision as of 10:39, 1 May 2008
Line 5:		Line 5:
	2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])		2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])

	3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, ~~we state to have~~ one cycle only), e.g.:		3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, for one cycle only), e.g.:

	Minimization		Minimization

2008-05-01T10:38:51Z

2008-05-01T10:37:27Z

2008-05-01T10:36:53Z

← Older revision		Revision as of 10:36, 1 May 2008
Line 3:		Line 3:
	1. ''coords.inpcrd'' -- file with coordinates		1. ''coords.inpcrd'' -- file with coordinates

	2. ''coords.prmtop'' -- topology file (see [[http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here]])		2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here])

	3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.:		3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.: