hlamc.pl - Revision history

Edit: /* Options */

2009-07-29T02:59:28Z

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Edit at 02:54, 29 July 2009

2009-07-29T02:54:23Z

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2009-07-29T02:51:32Z

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2009-07-29T02:49:56Z

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Feig at 22:51, 7 January 2009

2009-01-07T22:51:15Z

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@@ Line 56: / Line 56: @@
 ; -seq file : MONSSTER sequence file
 ; -par name=value[,...] : overall simulation parameters
-; -latpar name=value[,...] : lattice simulation parameters
+; -latpar name=value[,...] : MONSSTER lattice simulation parameters
-; -aapar name=value[,...] : all-atom simulation parameters
+; -aapar name=value[,...] : CHARMM all-atom simulation parameters
-; -evalpar name=value[,...] : energy evaluation parameters
+; -evalpar name=value[,...] : CHARMM energy evaluation parameters
 ; -dir name : output directory name
 ; -enstag name : tag for ensemble
 ; -log file : log file name
-; -evallog file : log file name for energy evaluation
+; -evallog file : CHARMM log file name for energy evaluation
-; -aalog file : log file name for all-atom simulation
+; -aalog file : CHARMM log file name for all-atom simulation
 == Examples ==

@@ Line 59: / Line 59: @@
 ; -aapar name=value[,...] : all-atom simulation parameters
 ; -evalpar name=value[,...] : energy evaluation parameters
 == Examples ==

@@ Line 53: / Line 53: @@
 ; -help : usage information
+; -n runs : number of cycles
 == Examples ==

@@ Line 36: / Line 36: @@
 Lattice simulations require a MONSSTER sequence file as input with <B>-seq</B>. Other lattice simulation
 parameters such as the number of lattice simulation Monte Carlo cycles, the internal temperature or
-potential component scaling factors as listed in <docmark>geninput.pl</docmark> are given with <B>-latpar</B>.<BR>
+potential component scaling factors as listed in [[geninput.pl]] are given with <B>-latpar</B>.<BR>
 All-atom simulation parameters are set with <B>-aapar</B>. The complete list of possible parameters is
-given [http://mmtsb.scripps.edu/cgi-bin/charmmpar here]. Minimization runs are
+given [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters here]. Minimization runs are
 performed if <font color=#508060>sdsteps</font> and/or <font color=#508060>minsteps</font> are set to non-zero values. Molecular dynamics
 is turned off by default but will be performed if <font color=#508060>dynsteps</font> is set. Parameters for a separate

@@ Line 33: / Line 33: @@
 a simple vacuum energy function may be sufficient for restrained all-atom minimizations and short molecular dynamics
 runs. The number of total Monte Carlo cycles is set with <B>-n</B>.<BR>
 Lattice simulations require a MONSSTER sequence file as input with <B>-seq</B>. Other lattice simulation
 parameters such as the number of lattice simulation Monte Carlo cycles, the internal temperature or
 potential component scaling factors as listed in <docmark>geninput.pl</docmark> are given with <B>-latpar</B>.<BR>
 All-atom simulation parameters are set with <B>-aapar</B>. The complete list of possible parameters is
-given <A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>. Minimization runs are
+given [http://mmtsb.scripps.edu/cgi-bin/charmmpar here]. Minimization runs are
 performed if <font color=#508060>sdsteps</font> and/or <font color=#508060>minsteps</font> are set to non-zero values. Molecular dynamics
 is turned off by default but will be performed if <font color=#508060>dynsteps</font> is set. Parameters for a separate
 energy evaluation are set with <B>-evalpar</B>.<BR>
 All output is written to the current directory unless a different directory is specified with <B>-dir</B>.
 Structures that are accepted at the end of a Monte Carlo cycle are saved into an ensemble under the same
 directory. The tag that is used can be set with <B>-enstag</B>.<BR>
 Log files for the all-atom simulation part, all-atom evaluation, and overall hybrid sampling are generated
 if the options <B>-aalog</B>, <B>-evallog</B>, or <B>-log</B> are used.<BR>

@@ Line 20: / Line 20: @@
 However, one faces the same barriers due to steric hindrance as in conventional all-atom simulations
 that are easily overcome with the reduced lattice model in the first mode.<BR>
 The default mode is "free". It can be selected with the <font color=#508060>mode</font> keyword of the <B>-par</B> option.
 Other parameters are the Metropolis 'temperature' in units of kcal/mol that is set with <font color=#508060>mctemp</font>,

@@ Line 6: / Line 6: @@
 == Description ==
-This utility is used for running single hybrid lattice/all-atom simulations. A replica exchange
+This utility is used for running single hybrid lattice/all-atom simulations. A replica exchange version [[hlamcrex.pl]] is also available.<BR>
-version <docmark>hlamcrex.pl</docmark> is also available.<BR>
 Two Monte Carlo simulation schemes are available for hybrid simulations that combine lattice and all-atom models.
 In both modes lattice models are effectively simulated on an all-atom surface combining the advantages of
 reduced lattice models with a more accurate all-atom potential energy function.<BR>
 In the first mode, called the "free" mode, a Monte Carlo simulation cycle consists of a lattice simulation and all-atom
-reconstruction of the final lattice chain followed by all-atom minimization and molecular dynamics.
+reconstruction of the final lattice chain followed by all-atom minimization and molecular dynamics. The all-atom energy at the end of each cycle is used for accepting or rejecting conformations according to Metropolis criteria.<BR>
 The all-atom energy at the end of each cycle is used for accepting or rejecting conformations according to Metropolis
-criteria.<BR>
+In the second mode, called "coupled", lattice and all-atom simulations are more tightly coupled. Here, final conformations from very short lattice simulations are used for generating side chain center of mass restraints in continuous all-atom minimization or molecular dynamics runs. As in the first mode, all-atom energies are used for accepting or rejecting conformations in a Monte
 Carlo scheme. The advantage of the second method is that the all-atom structures remain mostly
 relaxed throughout the simulation while following the guiding restraints from the lattice simulations.

←Older revision		Revision as of 22:51, 7 January 2009
Line 1:		Line 1:
−	~~dummy~~	+	__NOTOC__
		+	== Usage ==
		+
		+	<mmtsbToolUsage cmd="hlamc.pl"></mmtsbToolUsage>
		+
		+	== Description ==
		+
		+	This utility is used for running single hybrid lattice/all-atom simulations. A replica exchange
		+	version <docmark>hlamcrex.pl</docmark> is also available.<BR>
		+	Two Monte Carlo simulation schemes are available for hybrid simulations that combine lattice and all-atom models.
		+	In both modes lattice models are effectively simulated on an all-atom surface combining the advantages of
		+	reduced lattice models with a more accurate all-atom potential energy function.<BR>
		+	In the first mode, called the "free" mode, a Monte Carlo simulation cycle consists of a lattice simulation and all-atom
		+	reconstruction of the final lattice chain followed by all-atom minimization and molecular dynamics.
		+	The all-atom energy at the end of each cycle is used for accepting or rejecting conformations according to Metropolis
		+	criteria.<BR>
		+	In the second mode, called "coupled", lattice and all-atom simulations are more tightly coupled.
		+	Here, final conformations from very short lattice simulations are used for generating side chain
		+	center of mass restraints in continuous all-atom minimization or molecular dynamics runs.
		+	As in the first mode, all-atom energies are used for accepting or rejecting conformations in a Monte
		+	Carlo scheme. The advantage of the second method is that the all-atom structures remain mostly
		+	relaxed throughout the simulation while following the guiding restraints from the lattice simulations.
		+	However, one faces the same barriers due to steric hindrance as in conventional all-atom simulations
		+	that are easily overcome with the reduced lattice model in the first mode.<BR>
		+	The default mode is "free". It can be selected with the <font color=#508060>mode</font> keyword of the <B>-par</B> option.
		+	Other parameters are the Metropolis 'temperature' in units of kcal/mol that is set with <font color=#508060>mctemp</font>,
		+	the force constant that is used for C-alpha restraints in the all-atom part during the "free" mode,
		+	the force constant used in the "coupled" mode for side chain center restraints,
		+	and two additional options <font color=#508060>[no]keepchain</font> and <font color=#508060>[no]eval</font>. The first one sets whether lattice simulations
		+	are continued from the final chain of the previous lattice run (<font color=#508060>keepchain</font>, default)
		+	or from a chain generated at the end of the all-atom simulation section (<font color=#508060>nokeepchain</font>).
		+	The second option controls whether a separate instance of CHARMM is used for evaluating all-atom energies at
		+	the end of the simulation cycle(<font color=#508060>eval</font> vs. <font color=#508060>noeval</font>). This is useful when a different,
		+	more costly function, e.g. using an implicit solvation term, should be used for evaluating energies while
		+	a simple vacuum energy function may be sufficient for restrained all-atom minimizations and short molecular dynamics
		+	runs. The number of total Monte Carlo cycles is set with <B>-n</B>.<BR>
		+	Lattice simulations require a MONSSTER sequence file as input with <B>-seq</B>. Other lattice simulation
		+	parameters such as the number of lattice simulation Monte Carlo cycles, the internal temperature or
		+	potential component scaling factors as listed in <docmark>geninput.pl</docmark> are given with <B>-latpar</B>.<BR>
		+	All-atom simulation parameters are set with <B>-aapar</B>. The complete list of possible parameters is
		+	given <A HREF="http://mmtsb.scripps.edu/cgi-bin/charmmpar" TARGET=cpar>here</A>. Minimization runs are
		+	performed if <font color=#508060>sdsteps</font> and/or <font color=#508060>minsteps</font> are set to non-zero values. Molecular dynamics
		+	is turned off by default but will be performed if <font color=#508060>dynsteps</font> is set. Parameters for a separate
		+	energy evaluation are set with <B>-evalpar</B>.<BR>
		+	All output is written to the current directory unless a different directory is specified with <B>-dir</B>.
		+	Structures that are accepted at the end of a Monte Carlo cycle are saved into an ensemble under the same
		+	directory. The tag that is used can be set with <B>-enstag</B>.<BR>
		+	Log files for the all-atom simulation part, all-atom evaluation, and overall hybrid sampling are generated
		+	if the options <B>-aalog</B>, <B>-evallog</B>, or <B>-log</B> are used.<BR>
		+
		+	== Options ==
		+
		+	; -help : usage information
		+
		+
		+	== Examples ==
		+
		+	<mmtsbToolExample cmd="hlamc.pl" set="/apps/mmtsb/bench/hlamc.pl-test/test1"></mmtsbToolExample>
		+
		+	<mmtsbToolExample cmd="hlamc.pl" set="/apps/mmtsb/bench/hlamc.pl-test/test2"></mmtsbToolExample>

←Older revision	Revision as of 12:04, 29 December 2008
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←Older revision	Revision as of 19:44, 24 December 2008
(No difference)