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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3998 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2010-04-14 15:35:27 +00:00
parent 1bd62084ae
commit 3922a1ac19
6 changed files with 27 additions and 26 deletions
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6
doc/Section_howto.html
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@ -402,7 +402,7 @@ r0 of OH bond = 0.9572 <BR>
theta of HOH angle = 104.52 <BR>
</P>
<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 <A HREF = "#Price">(Price)</A> for details:
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
@ -1458,4 +1458,8 @@ Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
</P>
<A NAME = "Price"></A>
<P><B>(Price)</B> Price and Brooks, J Chem Phys, 121, 10096 (2004).
</P>
</HTML>

5
doc/Section_howto.txt
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@ -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).

15
doc/Section_tools.html
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@ -193,16 +193,13 @@ README file for more information.
<H4><A NAME = "vmd"></A>lmp2vmd tool
</H4>
<P>The lmp2vmd sub-directory contains some scripts for converting LAMMPS
files into formats suitable for visualizing with the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/">VMD
package</A>.
<P>The lmp2vmd sub-directory contains a README.txt file that describes
details of scripts and plugin support within the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD
package</A> for visualizing LAMMPS
dump files.
</P>
<P>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.
</P>
<P>These scripts were written by Axel Kohlmeyer (akohlmey at
cmm.chem.upenn.edu) at U Penn.
<P>The VMD plugins and other supporting scripts were written by Axel
Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
</P>
<HR>

15
doc/Section_tools.txt
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@ -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

6
doc/dump.html
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@ -218,9 +218,9 @@ coordinate format that many codes can read.
</P>
<P>Note that DCD, XTC, and XYZ formatted files can be read directly by
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> (a popular molecular viewing
program). We are told VMD will also read LAMMPS <I>atom</I> 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 <A HREF = "Section_tools.html#vmd">this section</A> of the manual and
the tools/lmp2vmd/README.txt file for more information about support
in VMD for reading and visualizing LAMMPS dump files.
</P>
<HR>

6
doc/dump.txt
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@ -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