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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8119 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-05-22 13:56:16 +00:00
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44
doc/fix_restrain.html
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@ -13,43 +13,51 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>fix ID group-ID restrain Kstart Kstop keyword value(s) <PRE>fix ID group-ID restrain keyword args ...
</PRE> </PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command <UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>restrain = style name of this fix command <LI>restrain = style name of this fix command
<LI>Kstart, Kstop = restraint coefficient at start/end of run (energy <LI>one or more keyword/arg pairs may be appended
units)
<LI>one keyword with one or more sets of parameter values may be appended to args <LI>keyword = <I>bond</I> or <I>angle</I> or <I>dihedral</I>
<LI>keyword = <I>dihedral</I> <PRE> <I>bond</I> args = atom1 atom2 Kstart Kstop r0
atom1,atom2 = IDs of 2 atoms in bond
<PRE> <I>dihedral</I> value = atom1 atom2 atom3 atom4 target Kstart,Kstop = restraint coefficients at start/end of run (energy units)
atom1,atom2,atom3,atom4 = IDs of 4 atoms in restrained dihedral r0 = target value for bond distance (distance units)
target = target value for specified dihedral angle (degrees) <I>angle</I> args = atom1 atom2 atom3 Kstart Kstop theta
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta = target value for angle theta (degrees)
<I>bond</I> args = atom1 atom2 atom3 atom4 Kstart Kstop phi
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
phi = target value for dihedral angle phi (degrees)
</PRE> </PRE>
</UL> </UL>
<P><B>Examples:</B> <P><B>Examples:</B>
</P> </P>
<PRE>fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0 <PRE>fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
fix texas_holdem all restrain 0.0 2000.0 dihedral 1 2 3 4 120.0 1 2 3 5 -120.0 1 2 3 6 0.0 fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Restrain the motion of the specified atoms by making them part of a <P>Restrain the motion of the specified sets of atoms by making them part
bond or angle or dihedral interaction whose strength can vary over of bond or angle or dihedral interaction whose strength can vary over
time during a simulation. This is functionally equivalent to creating time during a simulation. This is functionally equivalent to creating
a bond or angle or dihedral for the atoms in a data file, as specified a bond or angle or dihedral for the same atoms in a data file, as
by the <A HREF = "read_data.html">read_data</A> command, albeit with a time-varying specified by the <A HREF = "read_data.html">read_data</A> command, albeit with a
pre-factor coefficient. For the purpose of forcefield time-varying pre-factor coefficient. For the purpose of forcefield
parameter-fitting or mapping a molecular potential energy surface, parameter-fitting or mapping a molecular potential energy surface,
this fix reduces the hassle and risk associated with modifying data this fix reduces the hassle and risk associated with modifying data
files. In other words, use this fix to temporarily force a molecule files. In other words, use this fix to temporarily force a molecule
to adopt a particular conformation. To form a permanent bond or angle to adopt a particular conformation. To create a permanent bond or
or dihedral, modify the data file. angle or dihedral, you should modify the data file.
</P> </P>
<P>The first example above applies a restraint to hold the dihedral angle <P>The first example above applies a restraint to hold the dihedral angle
formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant

43
doc/fix_restrain.txt
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@ -10,37 +10,46 @@ fix restrain command :h3
[Syntax:] [Syntax:]
fix ID group-ID restrain Kstart Kstop keyword value(s) :pre fix ID group-ID restrain keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l ID, group-ID are documented in "fix"_fix.html command :ulb,l
restrain = style name of this fix command :l restrain = style name of this fix command :l
Kstart, Kstop = restraint coefficient at start/end of run (energy one or more keyword/arg pairs may be appended :l
units) :l keyword = {bond} or {angle} or {dihedral} :l
one keyword with one or more sets of parameter values may be appended to args :l {bond} args = atom1 atom2 Kstart Kstop r0
keyword = {dihedral} :l atom1,atom2 = IDs of 2 atoms in bond
{dihedral} value = atom1 atom2 atom3 atom4 target Kstart,Kstop = restraint coefficients at start/end of run (energy units)
atom1,atom2,atom3,atom4 = IDs of 4 atoms in restrained dihedral r0 = target value for bond distance (distance units)
target = target value for specified dihedral angle (degrees) :pre {angle} args = atom1 atom2 atom3 Kstart Kstop theta
atom1,atom2,atom3 = IDs of 3 atoms in angle, atom2 = middle atom
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
theta = target value for angle theta (degrees)
{bond} args = atom1 atom2 atom3 atom4 Kstart Kstop phi
atom1,atom2,atom3,atom4 = IDs of 4 atoms in dihedral in linear order
Kstart,Kstop = restraint coefficients at start/end of run (energy units)
phi = target value for dihedral angle phi (degrees) :pre
:ule :ule
[Examples:] [Examples:]
fix holdem all restrain 2000.0 2000.0 dihedral 1 2 3 4 120.0 fix holdem all restrain bond 45 48 2000.0 2000.0 2.75
fix texas_holdem all restrain 0.0 2000.0 dihedral 1 2 3 4 120.0 1 2 3 5 -120.0 1 2 3 6 0.0 :pre fix holdem all restrain dihedral 1 2 3 4 2000.0 2000.0 120.0
fix holdem all restrain bond 45 48 2000.0 2000.0 2.75 dihedral 1 2 3 4 2000.0 2000.0 120.0
fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 0.0 2000.0 -120.0 dihedral 1 2 3 6 0.0 2000.0 0.0 :pre
[Description:] [Description:]
Restrain the motion of the specified atoms by making them part of a Restrain the motion of the specified sets of atoms by making them part
bond or angle or dihedral interaction whose strength can vary over of bond or angle or dihedral interaction whose strength can vary over
time during a simulation. This is functionally equivalent to creating time during a simulation. This is functionally equivalent to creating
a bond or angle or dihedral for the atoms in a data file, as specified a bond or angle or dihedral for the same atoms in a data file, as
by the "read_data"_read_data.html command, albeit with a time-varying specified by the "read_data"_read_data.html command, albeit with a
pre-factor coefficient. For the purpose of forcefield time-varying pre-factor coefficient. For the purpose of forcefield
parameter-fitting or mapping a molecular potential energy surface, parameter-fitting or mapping a molecular potential energy surface,
this fix reduces the hassle and risk associated with modifying data this fix reduces the hassle and risk associated with modifying data
files. In other words, use this fix to temporarily force a molecule files. In other words, use this fix to temporarily force a molecule
to adopt a particular conformation. To form a permanent bond or angle to adopt a particular conformation. To create a permanent bond or
or dihedral, modify the data file. angle or dihedral, you should modify the data file.
The first example above applies a restraint to hold the dihedral angle The first example above applies a restraint to hold the dihedral angle
formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant