git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3409 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -28,7 +28,10 @@
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on = "unwrapped" coordinates using the image flags used
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<I>fscale</I> arg = factor
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factor = floating point number to scale IMD forces (default: 1.0)
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<I>trate</I> arg = transmission rate of coordinate data sets (default: 1)
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<I>trate</I> arg = transmission rate of coordinate data sets (default: 1)
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<I>nowait</I> arg = <I>on</I> or <I>off</I>
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off = LAMMPS waits to be connected to an IMD client before continuing (default)
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on = LAMMPS listens for an IMD client, but continues with the run
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</PRE>
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</UL>
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@ -50,58 +53,66 @@ Institute for Advanced Science and Technology at the University of
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Illinois at Urbana-Champaign. We thank them for providing a software
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interface that allows codes like LAMMPS to hook to <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
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</P>
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<P>Upon initialization of the fix, it will open a communication port
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on the node with MPI task 0 and wait for an incoming connection.
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As soon as an IMD client is connected, the simulation will continue
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and the fix will send the current coordinates of the fix's group
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to the IMD client at every trate MD step. When using r-RESPA, trate
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applies to the steps of the outmost RESPA level.
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During a run with an active IMD connection also the IMD client can
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request to apply forces to selected atoms of the fix group.
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<P>Upon initialization of the fix, it will open a communication port on
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the node with MPI task 0 and wait for an incoming connection. As soon
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as an IMD client is connected, the simulation will continue and the
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fix will send the current coordinates of the fix's group to the IMD
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client at every trate MD step. When using r-RESPA, trate applies to
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the steps of the outmost RESPA level. During a run with an active IMD
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connection also the IMD client can request to apply forces to selected
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atoms of the fix group.
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</P>
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<P>The port number selected must be an available network port number.
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On many machines, port numbers < 1024 are reserved for accounts with
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system manager privilege and specific applications. If multiple imd
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fixes would be active at the same time, each needs to use a different
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<P>The port number selected must be an available network port number. On
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many machines, port numbers < 1024 are reserved for accounts with
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system manager privilege and specific applications. If multiple imd
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fixes would be active at the same time, each needs to use a different
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port number.
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</P>
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<P>The <I>trate</I> keyword allows to select how often the coordinate data
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is sent to the IMD client. It can also be changed on request of
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the IMD client through an IMD protocol message.
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The <I>unwrap</I> keyword allows to send "unwrapped" coordinates to
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the IMD client that undo the wrapping back of coordinates into
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the principle unit cell, as done by default in LAMMPS.
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The <I>fscale</I> keyword allows to apply a scaling factor to forces
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transmitted by the IMD client. The IMD protocols stipulates that
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forces are transferred in kcal/mol/angstrom under the assumption
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that coordinates are given in angstrom. For LAMMPS runs with
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different units or as a measure to tweak the forces generated
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by the manipulation of the IMD client, this option allows to
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make adjustments.
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<P>The <I>nowait</I> keyword controls the behavior of the fix when no IMD
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client is connected. With the default setting of <I>off</I>, LAMMPS will
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wait until a connection is made before continuing with the
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execution. Setting <I>nowait</I> to <I>on</I> will have the LAMMPS code be ready
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to connect to a client, but continue with the simulation. This can for
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example be used to monitor the progress of an ongoing calculation
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without the need to be permanently connected or having to download a
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trajectory file.
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</P>
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<P>To connect VMD to a waiting LAMMPS simulation on the same
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machine with fix imd enabled, one needs to start VMD and load
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a coordinate or topology file that matches the fix group.
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When the VMD command prompts appears, one types the command line:
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<P>The <I>trate</I> keyword allows to select how often the coordinate data is
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sent to the IMD client. It can also be changed on request of the IMD
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client through an IMD protocol message. The <I>unwrap</I> keyword allows
|
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to send "unwrapped" coordinates to the IMD client that undo the
|
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wrapping back of coordinates into the principle unit cell, as done by
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default in LAMMPS. The <I>fscale</I> keyword allows to apply a scaling
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factor to forces transmitted by the IMD client. The IMD protocols
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stipulates that forces are transferred in kcal/mol/angstrom under the
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assumption that coordinates are given in angstrom. For LAMMPS runs
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with different units or as a measure to tweak the forces generated by
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the manipulation of the IMD client, this option allows to make
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adjustments.
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</P>
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<P>To connect VMD to a listening LAMMPS simulation on the same machine
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with fix imd enabled, one needs to start VMD and load a coordinate or
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topology file that matches the fix group. When the VMD command
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prompts appears, one types the command line:
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</P>
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<PRE>imd connect localhost 5678
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</PRE>
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<P>This assumes that <I>fix imd</I> was started with 5678 as a port
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number for the IMD protocol.
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</P>
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<P>The steps to do interactive manipulation of a running simulation
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in VMD are the following:
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<P>The steps to do interactive manipulation of a running simulation in
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VMD are the following:
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</P>
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<P>In the Mouse menu of the VMD Main window, select "Mouse -> Force -> Atom".
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You may alternately select "Residue", or "Fragment" to apply forces to
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whole residues or fragments. Your mouse can now be used to apply forces
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to your simulation. Click on an atom, residue, or fragment and drag to
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apply a force. Click quickly without moving the mouse to turn the force
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off. You can also use a variety of 3D position trackers to apply forces
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to your simulation. Trackers with force-feedback such as the Sensable
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PHANTOM allow you to feel the forces you are applying to your molecules,
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as if they were real objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> for
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more details.
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<P>In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
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Atom". You may alternately select "Residue", or "Fragment" to apply
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forces to whole residues or fragments. Your mouse can now be used to
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apply forces to your simulation. Click on an atom, residue, or
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fragment and drag to apply a force. Click quickly without moving the
|
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mouse to turn the force off. You can also use a variety of 3D position
|
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trackers to apply forces to your simulation. Trackers with
|
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force-feedback such as the Sensable PHANTOM allow you to feel the
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forces you are applying to your molecules, as if they were real
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objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> for more details.
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</P>
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<P>If IMD control messages are received, a line of text describing the
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message and its effect will be printed to the LAMMPS output screen, if
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@ -133,8 +144,8 @@ group the fix is applied to. The fix internally sorts atom IDs by
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ascending integer value; in VMD (and thus the IMD protocol) those will
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be assigned 0-based consecutive index numbers.
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</P>
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<P>When using multiple active IMD connections at the same time,
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each needs to use a different port number.
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<P>When using multiple active IMD connections at the same time, each
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needs to use a different port number.
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</P>
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<P><B>Related commands:</B> none
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</P>
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@ -21,7 +21,10 @@ keyword = {unwrap} or {fscale} or {trate} :l
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on = "unwrapped" coordinates using the image flags used
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{fscale} arg = factor
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factor = floating point number to scale IMD forces (default: 1.0)
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{trate} arg = transmission rate of coordinate data sets (default: 1) :pre
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{trate} arg = transmission rate of coordinate data sets (default: 1)
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{nowait} arg = {on} or {off}
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off = LAMMPS waits to be connected to an IMD client before continuing (default)
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on = LAMMPS listens for an IMD client, but continues with the run :pre
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:ule
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[Examples:]
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@ -42,58 +45,66 @@ Institute for Advanced Science and Technology at the University of
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Illinois at Urbana-Champaign. We thank them for providing a software
|
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interface that allows codes like LAMMPS to hook to "VMD"_VMD.
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|
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Upon initialization of the fix, it will open a communication port
|
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on the node with MPI task 0 and wait for an incoming connection.
|
||||
As soon as an IMD client is connected, the simulation will continue
|
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and the fix will send the current coordinates of the fix's group
|
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to the IMD client at every trate MD step. When using r-RESPA, trate
|
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applies to the steps of the outmost RESPA level.
|
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During a run with an active IMD connection also the IMD client can
|
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request to apply forces to selected atoms of the fix group.
|
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Upon initialization of the fix, it will open a communication port on
|
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the node with MPI task 0 and wait for an incoming connection. As soon
|
||||
as an IMD client is connected, the simulation will continue and the
|
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fix will send the current coordinates of the fix's group to the IMD
|
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client at every trate MD step. When using r-RESPA, trate applies to
|
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the steps of the outmost RESPA level. During a run with an active IMD
|
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connection also the IMD client can request to apply forces to selected
|
||||
atoms of the fix group.
|
||||
|
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The port number selected must be an available network port number.
|
||||
On many machines, port numbers < 1024 are reserved for accounts with
|
||||
system manager privilege and specific applications. If multiple imd
|
||||
fixes would be active at the same time, each needs to use a different
|
||||
The port number selected must be an available network port number. On
|
||||
many machines, port numbers < 1024 are reserved for accounts with
|
||||
system manager privilege and specific applications. If multiple imd
|
||||
fixes would be active at the same time, each needs to use a different
|
||||
port number.
|
||||
|
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The {trate} keyword allows to select how often the coordinate data
|
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is sent to the IMD client. It can also be changed on request of
|
||||
the IMD client through an IMD protocol message.
|
||||
The {unwrap} keyword allows to send "unwrapped" coordinates to
|
||||
the IMD client that undo the wrapping back of coordinates into
|
||||
the principle unit cell, as done by default in LAMMPS.
|
||||
The {fscale} keyword allows to apply a scaling factor to forces
|
||||
transmitted by the IMD client. The IMD protocols stipulates that
|
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forces are transferred in kcal/mol/angstrom under the assumption
|
||||
that coordinates are given in angstrom. For LAMMPS runs with
|
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different units or as a measure to tweak the forces generated
|
||||
by the manipulation of the IMD client, this option allows to
|
||||
make adjustments.
|
||||
The {nowait} keyword controls the behavior of the fix when no IMD
|
||||
client is connected. With the default setting of {off}, LAMMPS will
|
||||
wait until a connection is made before continuing with the
|
||||
execution. Setting {nowait} to {on} will have the LAMMPS code be ready
|
||||
to connect to a client, but continue with the simulation. This can for
|
||||
example be used to monitor the progress of an ongoing calculation
|
||||
without the need to be permanently connected or having to download a
|
||||
trajectory file.
|
||||
|
||||
To connect VMD to a waiting LAMMPS simulation on the same
|
||||
machine with fix imd enabled, one needs to start VMD and load
|
||||
a coordinate or topology file that matches the fix group.
|
||||
When the VMD command prompts appears, one types the command line:
|
||||
The {trate} keyword allows to select how often the coordinate data is
|
||||
sent to the IMD client. It can also be changed on request of the IMD
|
||||
client through an IMD protocol message. The {unwrap} keyword allows
|
||||
to send "unwrapped" coordinates to the IMD client that undo the
|
||||
wrapping back of coordinates into the principle unit cell, as done by
|
||||
default in LAMMPS. The {fscale} keyword allows to apply a scaling
|
||||
factor to forces transmitted by the IMD client. The IMD protocols
|
||||
stipulates that forces are transferred in kcal/mol/angstrom under the
|
||||
assumption that coordinates are given in angstrom. For LAMMPS runs
|
||||
with different units or as a measure to tweak the forces generated by
|
||||
the manipulation of the IMD client, this option allows to make
|
||||
adjustments.
|
||||
|
||||
To connect VMD to a listening LAMMPS simulation on the same machine
|
||||
with fix imd enabled, one needs to start VMD and load a coordinate or
|
||||
topology file that matches the fix group. When the VMD command
|
||||
prompts appears, one types the command line:
|
||||
|
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imd connect localhost 5678 :pre
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||||
|
||||
This assumes that {fix imd} was started with 5678 as a port
|
||||
number for the IMD protocol.
|
||||
|
||||
The steps to do interactive manipulation of a running simulation
|
||||
in VMD are the following:
|
||||
The steps to do interactive manipulation of a running simulation in
|
||||
VMD are the following:
|
||||
|
||||
In the Mouse menu of the VMD Main window, select "Mouse -> Force -> Atom".
|
||||
You may alternately select "Residue", or "Fragment" to apply forces to
|
||||
whole residues or fragments. Your mouse can now be used to apply forces
|
||||
to your simulation. Click on an atom, residue, or fragment and drag to
|
||||
apply a force. Click quickly without moving the mouse to turn the force
|
||||
off. You can also use a variety of 3D position trackers to apply forces
|
||||
to your simulation. Trackers with force-feedback such as the Sensable
|
||||
PHANTOM allow you to feel the forces you are applying to your molecules,
|
||||
as if they were real objects. See the "VMD IMD Homepage"_imdvmd for
|
||||
more details.
|
||||
In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
|
||||
Atom". You may alternately select "Residue", or "Fragment" to apply
|
||||
forces to whole residues or fragments. Your mouse can now be used to
|
||||
apply forces to your simulation. Click on an atom, residue, or
|
||||
fragment and drag to apply a force. Click quickly without moving the
|
||||
mouse to turn the force off. You can also use a variety of 3D position
|
||||
trackers to apply forces to your simulation. Trackers with
|
||||
force-feedback such as the Sensable PHANTOM allow you to feel the
|
||||
forces you are applying to your molecules, as if they were real
|
||||
objects. See the "VMD IMD Homepage"_imdvmd for more details.
|
||||
|
||||
If IMD control messages are received, a line of text describing the
|
||||
message and its effect will be printed to the LAMMPS output screen, if
|
||||
@ -124,8 +135,8 @@ group the fix is applied to. The fix internally sorts atom IDs by
|
||||
ascending integer value; in VMD (and thus the IMD protocol) those will
|
||||
be assigned 0-based consecutive index numbers.
|
||||
|
||||
When using multiple active IMD connections at the same time,
|
||||
each needs to use a different port number.
|
||||
When using multiple active IMD connections at the same time, each
|
||||
needs to use a different port number.
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
|
||||
Reference in New Issue
Block a user