diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 521ab237e6..7aff4366c9 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -402,7 +402,7 @@ r0 of OH bond = 0.9572
theta of HOH angle = 104.52

These are the parameters to use for TIP3P with a long-range Coulombic -solver (Ewald or PPPM in LAMMPS): +solver (Ewald or PPPM in LAMMPS), see (Price) for details:

O mass = 15.9994
H mass = 1.008
@@ -1458,4 +1458,8 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).

(Jorgensen) Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983).

+ + +

(Price) Price and Brooks, J Chem Phys, 121, 10096 (2004). +

diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index c6396e3534..c6000a0388 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -398,7 +398,7 @@ K of HOH angle = 55 theta of HOH angle = 104.52 :all(b),p These are the parameters to use for TIP3P with a long-range Coulombic -solver (Ewald or PPPM in LAMMPS): +solver (Ewald or PPPM in LAMMPS), see "(Price)"_#Price for details: O mass = 15.9994 H mass = 1.008 :all(b),p @@ -1441,3 +1441,6 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998). :link(Jorgensen) [(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983). + +:link(Price) +[(Price)] Price and Brooks, J Chem Phys, 121, 10096 (2004). diff --git a/doc/Section_tools.html b/doc/Section_tools.html index f2f3d54a79..59cf12fd91 100644 --- a/doc/Section_tools.html +++ b/doc/Section_tools.html @@ -193,16 +193,13 @@ README file for more information.

lmp2vmd tool

-

The lmp2vmd sub-directory contains some scripts for converting LAMMPS -files into formats suitable for visualizing with the VMD -package. +

The lmp2vmd sub-directory contains a README.txt file that describes +details of scripts and plugin support within the VMD +package for visualizing LAMMPS +dump files.

-

One script extracts bond topology info from a LAMMPS data file. A -second script attached amino acid (residue) information to what is -extracted from a data file. See the README file for more information. -

-

These scripts were written by Axel Kohlmeyer (akohlmey at -cmm.chem.upenn.edu) at U Penn. +

The VMD plugins and other supporting scripts were written by Axel +Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.


diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt index 934590b382..1fbf364ba9 100644 --- a/doc/Section_tools.txt +++ b/doc/Section_tools.txt @@ -189,16 +189,13 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov). lmp2vmd tool :h4,link(vmd) -The lmp2vmd sub-directory contains some scripts for converting LAMMPS -files into formats suitable for visualizing with the "VMD -package"_http://www.ks.uiuc.edu/Research/vmd/. +The lmp2vmd sub-directory contains a README.txt file that describes +details of scripts and plugin support within the "VMD +package"_http://www.ks.uiuc.edu/Research/vmd for visualizing LAMMPS +dump files. -One script extracts bond topology info from a LAMMPS data file. A -second script attached amino acid (residue) information to what is -extracted from a data file. See the README file for more information. - -These scripts were written by Axel Kohlmeyer (akohlmey at -cmm.chem.upenn.edu) at U Penn. +The VMD plugins and other supporting scripts were written by Axel +Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn. :line diff --git a/doc/dump.html b/doc/dump.html index 41eb68ba94..2dac4ae213 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -218,9 +218,9 @@ coordinate format that many codes can read.

Note that DCD, XTC, and XYZ formatted files can be read directly by VMD (a popular molecular viewing -program). We are told VMD will also read LAMMPS atom style dump -files since someone has added a LAMMPS format plug-in to VMD. It may -require an initial snapshot from an XYZ formatted file to get started. +program). See this section of the manual and +the tools/lmp2vmd/README.txt file for more information about support +in VMD for reading and visualizing LAMMPS dump files.


diff --git a/doc/dump.txt b/doc/dump.txt index 32c75b581a..6751d510a1 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -208,9 +208,9 @@ coordinate format that many codes can read. Note that DCD, XTC, and XYZ formatted files can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd (a popular molecular viewing -program). We are told VMD will also read LAMMPS {atom} style dump -files since someone has added a LAMMPS format plug-in to VMD. It may -require an initial snapshot from an XYZ formatted file to get started. +program). See "this section"_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. :line