git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12818 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_gle.html

@@ -50,7 +50,8 @@ vibrational modes in the system to inexpensive (approximate)
 modelling of nuclear quantum effects. Contrary to 
 <A HREF = "fix_langevin.html">fix langevin</A>, this fix performs both 
 thermostatting and evolution of the Hamiltonian equations of motion, so it 
-does not need to be used together with <A HREF = "fix_nve.html">fix nve</A>.
+should not be used together with <A HREF = "fix_nve.html">fix nve</A> -- at least not 
+on the same atom groups. 
 </P>
 <P>Each degree of freedom in the thermostatted group is supplemented
 with Ns additional degrees of freedom s, and the equations of motion
@@ -93,6 +94,14 @@ generate its own unique seed and its own stream of random numbers.
 Thus the dynamics of the system will not be identical on two runs on
 different numbers of processors. 
 </P>
+<P>Note also that the Generalized Langevin Dynamics scheme that is 
+implemented by the <A HREF = "fix_gld.html">fix gld</A> scheme is closely related
+to the present one. In fact, it should be always possible to cast the
+Prony series form of the memory kernel used by GLD into an appropriate
+input matrix for <A HREF = "fix_gle.html">fix_gle</A>. While the GLE scheme is more
+general, the form used by <A HREF = "fix_gld.html">fix gld</A> can be more directly
+related to the representation of an implicit solvent environment. 
+</P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
 <P>The instantaneous values of the extended variables are written to
@@ -127,6 +136,11 @@ with rigid bodies, SHAKE or RATTLE. It is expected that all the
 thermostatted degrees of freedom are fully flexible, and the sampled
 ensemble will not be correct otherwise.
 </P>
+<P>In order to perform constant-pressure simulations please use 
+<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>, rather than 
+<A HREF = "fix_npt.html">fix_npt</A>, to avoid duplicate integration of the
+equations of motion. 
+</P>
 <P>This fix is part of the USER-MISC package.  It is only enabled if LAMMPS
 was built with that package.  See the <A HREF = "Section_start.html#start_3">Making
 LAMMPS</A> section for more info.

doc/fix_gle.txt

@@ -40,7 +40,8 @@ vibrational modes in the system to inexpensive (approximate)
 modelling of nuclear quantum effects. Contrary to 
 "fix langevin"_fix_langevin.html, this fix performs both 
 thermostatting and evolution of the Hamiltonian equations of motion, so it 
-does not need to be used together with "fix nve"_fix_nve.html.
+should not be used together with "fix nve"_fix_nve.html -- at least not 
+on the same atom groups. 
 
 Each degree of freedom in the thermostatted group is supplemented
 with Ns additional degrees of freedom s, and the equations of motion
@@ -83,6 +84,14 @@ generate its own unique seed and its own stream of random numbers.
 Thus the dynamics of the system will not be identical on two runs on
 different numbers of processors. 
 
+Note also that the Generalized Langevin Dynamics scheme that is 
+implemented by the "fix gld"_fix_gld.html scheme is closely related
+to the present one. In fact, it should be always possible to cast the
+Prony series form of the memory kernel used by GLD into an appropriate
+input matrix for "fix_gle"_fix_gle.html. While the GLE scheme is more
+general, the form used by "fix gld"_fix_gld.html can be more directly
+related to the representation of an implicit solvent environment. 
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 The instantaneous values of the extended variables are written to
@@ -117,6 +126,11 @@ with rigid bodies, SHAKE or RATTLE. It is expected that all the
 thermostatted degrees of freedom are fully flexible, and the sampled
 ensemble will not be correct otherwise.
 
+In order to perform constant-pressure simulations please use 
+"fix press/berendsen"_fix_press_berendsen.html, rather than 
+"fix_npt"_fix_npt.html, to avoid duplicate integration of the
+equations of motion. 
+
 This fix is part of the USER-MISC package.  It is only enabled if LAMMPS
 was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.