fix problems with references

doc/src/compute_modify.txt

@@ -54,7 +54,7 @@ adding atoms or molecules to the system (see the "fix
 pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix
 gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost
 (e.g. due to exiting the simulation box or via "fix
-evaporation"_fix_evaporation.html), then this option should be used to
+evaporate"_fix_evaporate.html), then this option should be used to
 insure the temperature is correctly normalized.
 
 NOTE: The {extra} and {dynamic} keywords should not be used as they

doc/src/dump.txt

@@ -331,10 +331,7 @@ bonds and colors.
 
 Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
 can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-popular molecular viewing program.  See
-"Section 9"_Section_tools.html#vmd of the manual and the
-tools/lmp2vmd/README.txt file for more information about support in
-VMD for reading and visualizing LAMMPS dump files.
+popular molecular viewing program.
 
 :line
 

doc/src/fix_cmap.txt

@@ -27,7 +27,7 @@ fix_modify     myCMAP energy yes :pre
 This command enables CMAP crossterms to be added to simulations which
 use the CHARMM force field.  These are relevant for any CHARMM model
 of a peptide or protein sequences that is 3 or more amino-acid
-residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks for details,
+residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details,
 including the analytic energy expressions for CMAP interactions.  The
 CMAP crossterms add additional potential energy contributions to pairs
 of overlapping phi-psi dihedrals of amino-acids, which are important
@@ -128,5 +128,5 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
 [(Buck)] Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
 (2006).
 
-:link(Brooks)
+:link(Brooks2)
 [(Brooks)] Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).

doc/src/fix_modify.txt

@@ -91,7 +91,7 @@ their DOF are assumed to be constant.  If you are adding atoms or
 molecules to the system (see the "fix pour"_fix_pour.html, "fix
 deposit"_fix_deposit.html, and "fix gcmc"_fix_gcmc.html commands) or
 expect atoms or molecules to be lost (e.g. due to exiting the
-simulation box or via "fix evaporation"_fix_evaporation.html), then
+simulation box or via "fix evaporate"_fix_evaporate.html), then
 this option should be used to insure the temperature is correctly
 normalized.
 

doc/src/pair_charmm.txt

@@ -94,7 +94,7 @@ The newer styles with {charmmfsw} or {charmmfsh} in their name replace
 the energy switching with force switching (fsw) and force shifting
 (fsh) functions, for LJ and Coulombic interactions respectively.
 These follow the formulas and description given in
-"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks to minimize these
+"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks1 to minimize these
 artifacts.
 
 NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
@@ -248,7 +248,7 @@ the MOLECULE and KSPACE packages are installed by default.
 
 :line
 
-:link(Brooks)
+:link(Brooks1)
 [(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009).
 
 :link(pair-MacKerell)