git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11995 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/moltemplate/common/oplsaa/alternate_oplsaa_file/README_alternate_atom_numbers.txt

@@ -1,52 +0,0 @@
-MOST USERS CAN IGNORE THIS DIRECTORY.
-
-This is the original version of oplsaa.txt released with 
-moltemplate version 1.20.  Later on I decided to direct 
-users to the (hopefully current) version of the "oplsaa.prm" 
-file distributed with TINKER's force-field-explorer program.
-
-http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
-http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
-
-The original oplsaa.txt from moltemplate version 1.20 file is located here.
-Feel free to pick whichever one works well for your application, but 
-if you publish a paper using these parameters please cite TINKER,
-since that appears to be the source of all of these files.
-I think these are the relevant citations:
-
-Ponder, J. W., & Richards, F. M. (1987). "An efficient newton‐like method for molecular mechanics energy minimization of large molecules. Journal of Computational Chemistry", 8(7), 1016-1024.
-
-Ponder, J. W, (2004) "TINKER: Software tools for molecular design", http://dasher.wustl.edu/tinker/
-
-
-Here is a discussion of a difference between these two files:
-
->> On Fri, Apr 11, 2014 at 6:44 PM, Andrew Jewett <jewett.aij@gmail.com> wrote:
->> Jason
->> Lambert graciously wrote the "oplsaa_moltemplate.py" script and
->> provided the "oplsaa.txt" file which it reads as an input file (after
->> some minor manual editing on the part of the user).  I did some
->> googling, and I noticed that this file is very similar to the
->> "oplsaa.prm" file located at this web site:
->>
->> http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
->>
->> I suspect it uses the same parameter conventions.
->>
->> However I just realized that the two files are not identical.  (I am
->> emailing Jason now to ask about the difference.)
->>
->> Where did you get the data for the "oplsaa.txt" file?  More
->> specifically, where do the atom numbers come from?
-
->On Tue, Apr 15, 2014 at 6:06 PM, jason Lambert <jlamber9@gmail.com> wrote:
->To be honest I do not know the original source of the OPLSA force
-> field file. The file was provided by a graduate student from a group
-> I worked with and I did not question it other than spot checking with
-> values that were published.  I am surprised that the files are different.
-> Anyways, I am not aware of any logic to the observed switches in
-> the parameters. I did a diff -y on the two files and the difference is
-> primarily atom switching. The code works with either one though
-> so it is not a problem.  We can provide a link to the prm file as well.
-> I know I added some dihedrals explicitly but the ones I added were
-> already encompassed by the dihedrals containing wild cards.