diff --git a/doc/src/compute_modify.txt b/doc/src/compute_modify.txt index c26b5c2a5fe20273230b2c019982012efd048e48..9a2480ec0ac7fd7b584216a74355ed9b707c877e 100644 --- a/doc/src/compute_modify.txt +++ b/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 diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 1c65b1cdbf5833d0f80f97142b9ee1db84ad6fbd..cb9a5ba74112849fb220344a720ea5e66015fe75 100644 --- a/doc/src/dump.txt +++ b/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 diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index c943cde4897d65f9af50f2a765272144843bd0e3..5fcac589bef767f74140feb3bcd0a3503aad9f37 100644 --- a/doc/src/fix_cmap.txt +++ b/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). diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index 5e097bb34f6fde43a238b9ecfbdf9c50e6f3d98d..4e31092888bc1a9403ac9037dbccb84788e571f0 100644 --- a/doc/src/fix_modify.txt +++ b/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. diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index a3c93c7589889bc6b5fc92cd8f38d586004bcb87..e1101b4174e14a56bc91ea80849e97544b8074af 100644 --- a/doc/src/pair_charmm.txt +++ b/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)