Post-submission clean-up
Added Water.frc discussion, improved the integrator section, added references
Added two new figures
new updates
edits done
more revisions
add some keywords
added more revisions to the paper
starting to rearrange the prose after the intro.
added more tables.
added more tables
added in all of the general global keywords. Still need to add the zConstraint and minimizer keywords.
adding to the table
adding a separate file to work on the bass keywords.
finished removing the trajectory analysis. took out the rattle derivation. added a section concerning the creation of init files. currently working on a table of key words for the package.
fixed the makefile, and fixed some visuals on the schemes
finished cleaning up the old tex files
Just copied over the changes from the dissertation. Also converted the figures to pdf. All revisions now take place on the oopsePaper.tex file
NPTf complete, NPTxyz complete
NPTi complete
NPT work in progress
More DLM changes
more changes for integrators
Work on integrators
minor corrections to the previous commit
added changes into the Empirical Energy section
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Corrected .bib file entries
ran spell check, and fixed some little typos
worked listing schemes into the document
Adjusted the SSD part of the paper...
fixed some things in the periodic image part
Made changes to the rigid body stuff...
more changes to eam section.
More typo fixes.
Changed section on eam.
added new revisions
revision
Updated the rigid body and ssd sections
rotated the lipid figure added eam to the Emperical Energy
Added daw entry.
added a lennard jones section to the Emperical Energy section
Added rigid body discussion and added to .bib file...
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Periodic Boundary Conditions
started adding some changes from before break
reworked the directory structure to reflect the Outline of the paper. All major sections now have their own tex file
Started work on integrator stuff
New File
Formatting changes to get out of RevTex nonsense
dded my handwritten pages from 10-16-03
changed format to preprint article
Added zcons.tex
Just added to the make file...
Added the integrator.tex file with figure. This is the same as the ssdePaper, so it needs to be adjusted for the OOPSE paper. Also updated the oopse.bib file.
SSD portion of paper added (ssd.tex).
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Added parallel section of paper.
added a charmm citation to the bib file. finished adding all of the equations into DUFF.
added some text to DUFF, changed the preamble from two column to preprint format.
did some more work on DUFF.
added the lipid figure, and did some work on DUFF.
little changes to finish the port from make current to currMake
overhauled the makefile to build oopse.tex from the infiles rather than mess with includes. Also renamed header and footer to preamble and bibEnd respectively. make current has been replaced with currMake to tke a look at a single tex section.
added some work to DUFF
added a currMake script to replace the make current
played a little with the headers in DUFF
made some changes.
started working on DUFF
finished a rough draft of the dynamicProps section. added calculation sheme to the staticProps
added text to the analysis code.
trying to debug eqn references
added the main equations to the analysis section
edited the header to be a revtex style two column layout.
added a current.tex to allow for looking at your current work, just change the include to the current tex file also seperated all header info into header.tex so that oopse.tex and current.tex will behave the same.
This commit was generated by cvs2svn to compensate for changes in r662, which included commits to RCS files with non-trunk default branches.