Commit a241b2d0 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

fix problems with references

parent 61e7595a

doc/src/compute_modify.txt

+1 −1
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@@ -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

+1 −4
Original line number Diff line number Diff line
@@ -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

+2 −2
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@@ -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

+1 −1
Original line number Diff line number Diff line
@@ -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

+2 −2
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@@ -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)

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