Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F92792797
fix_spring_rg.html
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Nov 23, 18:33
Size
2 KB
Mime Type
text/html
Expires
Mon, Nov 25, 18:33 (1 d, 21 h)
Engine
blob
Format
Raw Data
Handle
22509776
Attached To
rLAMMPS lammps
fix_spring_rg.html
View Options
<HTML>
<CENTER><A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
</CENTER>
<HR>
<H3>
fix spring/rg command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
fix ID group-ID spring/rg K RG0
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"fix.html"
>
fix
</A>
command
<LI>
spring/rg = style name of this fix command
<LI>
K = harmonic force constant (force/distance units)
<LI>
RG0 = target radius of gyration to constrain to (distance units)
</UL>
<PRE>
if RG0 = NULL, use the current RG as the target value
</PRE>
<P><B>
Examples:
</B>
</P>
<PRE>
fix 1 protein spring/rg 5.0 10.0
fix 2 micelle spring/rg 5.0 NULL
</PRE>
<P><B>
Description:
</B>
</P>
<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>
<CENTER><IMG
SRC =
"Eqs/fix_spring_rg.jpg"
>
</CENTER>
<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>
<P><B>
Restart, fix_modify, output, run start/stop, minimize info:
</B>
</P>
<P>
No information about this fix is written to
<A
HREF =
"restart.html"
>
binary restart
files
</A>
. None of the
<A
HREF =
"fix_modify.html"
>
fix_modify
</A>
options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various
<A
HREF =
"Section_howto.html#howto_15"
>
output
commands
</A>
. No parameter of this fix can
be used with the
<I>
start/stop
</I>
keywords of the
<A
HREF =
"run.html"
>
run
</A>
command.
This fix is not invoked during
<A
HREF =
"minimize.html"
>
energy minimization
</A>
.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"fix_spring.html"
>
fix spring
</A>
,
<A
HREF =
"fix_spring_self.html"
>
fix spring/self
</A>
<A
HREF =
"fix_drag.html"
>
fix drag
</A>
,
<A
HREF =
"fix_smd.html"
>
fix smd
</A>
</P>
<P><B>
Default:
</B>
none
</P>
</HTML>
Event Timeline
Log In to Comment