2016-05-10 01:33:12 +08:00
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< li > fix spring/rg command< / li >
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< div class = "section" id = "fix-spring-rg-command" >
< span id = "index-0" > < / span > < h1 > fix spring/rg command< / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "n" > ID< / span > < span class = "n" > group< / span > < span class = "o" > -< / span > < span class = "n" > ID< / span > < span class = "n" > spring< / span > < span class = "o" > /< / span > < span class = "n" > rg< / span > < span class = "n" > K< / span > < span class = "n" > RG0< / span >
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< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < span class = "doc" > fix< / span > < / a > command< / li >
< li > spring/rg = style name of this fix command< / li >
< li > K = harmonic force constant (force/distance units)< / li >
< li > RG0 = target radius of gyration to constrain to (distance units)< / li >
< / ul >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "k" > if< / span > < span class = "n" > RG0< / span > < span class = "o" > =< / span > < span class = "n" > NULL< / span > < span class = "p" > ,< / span > < span class = "n" > use< / span > < span class = "n" > the< / span > < span class = "n" > current< / span > < span class = "n" > RG< / span > < span class = "k" > as< / span > < span class = "n" > the< / span > < span class = "n" > target< / span > < span class = "n" > value< / span >
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< h2 > Examples< / h2 >
< div class = "highlight-default" > < div class = "highlight" > < pre > < span > < / span > < span class = "n" > fix< / span > < span class = "mi" > 1< / span > < span class = "n" > protein< / span > < span class = "n" > spring< / span > < span class = "o" > /< / span > < span class = "n" > rg< / span > < span class = "mf" > 5.0< / span > < span class = "mf" > 10.0< / span >
< span class = "n" > fix< / span > < span class = "mi" > 2< / span > < span class = "n" > micelle< / span > < span class = "n" > spring< / span > < span class = "o" > /< / span > < span class = "n" > rg< / span > < span class = "mf" > 5.0< / span > < span class = "n" > NULL< / span >
< / pre > < / div >
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< div class = "section" id = "description" >
< h2 > Description< / h2 >
< p > Apply a harmonic restraining force to atoms in the group to affect
their central moment about the center of mass (radius of gyration).
This fix is useful to encourage a protein or polymer to fold/unfold
and also when sampling along the radius of gyration as a reaction
coordinate (i.e. for protein folding).< / p >
< p > The radius of gyration is defined as RG in the first formula. The
energy of the constraint and associated force on each atom is given by
the second and third formulas, when the group is at a different RG
than the target value RG0.< / p >
< img alt = "_images/fix_spring_rg.jpg" class = "align-center" src = "_images/fix_spring_rg.jpg" / >
< p > The (xi - center-of-mass) term is computed taking into account
periodic boundary conditions, m_i is the mass of the atom, and M is
the mass of the entire group. Note that K is thus a force constant
for the aggregate force on the group of atoms, not a per-atom force.< / p >
< p > If RG0 is specified as NULL, then the RG of the group is computed at
the time the fix is specified, and that value is used as the target.< / p >
2016-09-07 22:09:53 +08:00
< p > < strong > Restart, fix_modify, output, run start/stop, minimize info:< / strong > < / p >
2016-05-10 01:33:12 +08:00
< p > No information about this fix is written to < a class = "reference internal" href = "restart.html" > < span class = "doc" > binary restart files< / span > < / a > . None of the < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various < a class = "reference internal" href = "Section_howto.html#howto-15" > < span class = "std std-ref" > output commands< / span > < / a > . No parameter of this fix can
be used with the < em > start/stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < span class = "doc" > run< / span > < / a > command.
This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < span class = "doc" > energy minimization< / span > < / a > .< / p >
2016-06-18 07:24:05 +08:00
< p > The < a class = "reference internal" href = "fix_modify.html" > < span class = "doc" > fix_modify< / span > < / a > < em > respa< / em > option is supported by this
fix. This allows to set at which level of the < a class = "reference internal" href = "run_style.html" > < span class = "doc" > r-RESPA< / span > < / a >
integrator the fix is adding its forces. Default is the outermost level.< / p >
2016-05-10 01:33:12 +08:00
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< div class = "section" id = "restrictions" >
< h2 > Restrictions< / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< / h2 >
< p > < a class = "reference internal" href = "fix_spring.html" > < span class = "doc" > fix spring< / span > < / a > , < a class = "reference internal" href = "fix_spring_self.html" > < span class = "doc" > fix spring/self< / span > < / a >
< a class = "reference internal" href = "fix_drag.html" > < span class = "doc" > fix drag< / span > < / a > , < a class = "reference internal" href = "fix_smd.html" > < span class = "doc" > fix smd< / span > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
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