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