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117 commits

Author SHA1 Message Date
Kurt Glaesmann
061000a44c Remove the executable bit from non-executable files 2011-07-07 16:44:21 +00:00
Huub Van Dam
26cedba37c HvD: Apparently, I goofed recently when carrying over changes from the 
NWChem-6.0 release candidate to the development version. In this case
the amber parameters in the development version were actually more up-
to-date than those in the release. This check-in reverts the erroneous
changes I made. It will be followed by another check-in on the release
to migrate the changes in the other direction. 
I apologize unreservedly for any inconvience caused and hope that this
sequence of check-ins finalizes the MD code for the release.
 2010-09-09 15:29:42 +00:00
Marat Valiev
3716d847a7 adding QM/MM parameter file to user par directory 2010-09-02 17:33:00 +00:00
Huub Van Dam
296338416e HvD: Carried MD fixes from the nwchem-6.0 branch over to the development 
branch. These include:
- nwchem.F: always initialize the parallel environment data as this is needed
            by the fft-s.
- ARG_N.*: fix of the CB charge.
- test cases: updates to reference data.
 2010-08-30 18:24:36 +00:00
Tjerk Straatsma
7e70e0333e Fixed charge on CB 2010-04-27 21:32:21 +00:00
Kurt Glaesmann
2e8dfdb6cc Fix sgm files to match frg file charges (they had old amber charges) 
HIP_N,ARG_N,LYS_N,THR_N only
 2009-12-08 18:51:27 +00:00
Kurt Glaesmann
ba6331f9d7 Update sgm files to newer format 2009-10-06 18:25:58 +00:00
Kurt Glaesmann
6b5d731a73 NE is neon, not N type E 2009-10-06 18:25:02 +00:00
Kurt Glaesmann
74601f3c32 Add newer CHARMM forcefields to NWChem 2009-10-06 18:24:38 +00:00
Kurt Glaesmann
1731c8db29 Update frg files to match CHARMM charges. Last digit was missing in some 2009-09-10 22:07:28 +00:00
Kurt Glaesmann
e6298ec6fb Update frg files to newest file format (add column of zeros) 2009-08-26 17:21:53 +00:00
Kurt Glaesmann
7971e1cccf Update frg files to newest file format (add column of zeros) 2009-08-26 17:07:32 +00:00
Kurt Glaesmann
84d141733d Change "segment" to "fragment" in *.frg files-the comment line was wrong 2009-08-26 17:04:37 +00:00
Kurt Glaesmann
c6657b5412 Change "segment" to "fragment" in *.frg files-the comment line was wrong 2009-08-26 17:04:26 +00:00
Kurt Glaesmann
8c4fec2be4 Update segment files to current file format 2009-08-26 17:02:37 +00:00
Kurt Glaesmann
8bb6e181cf Update segment files to current file format 2009-08-26 17:01:44 +00:00
Kurt Glaesmann
9e40ac5ee3 Update segment files to current file format 2009-08-26 17:01:22 +00:00
Kurt Glaesmann
009071b3ec Update segment files to current file format 2009-08-26 17:01:07 +00:00
Kurt Glaesmann
24b4d871e4 Revert 2009-07-16 17:57:48 +00:00
Kurt Glaesmann
93dde91e58 Revert 2009-07-16 17:56:22 +00:00
Kurt Glaesmann
e7b65d6b02 Don't store sgm files in SVN 2009-07-16 17:43:35 +00:00
Kurt Glaesmann
3d822c9655 Don't store sgm files in SVN 2009-07-16 17:39:18 +00:00
Kurt Glaesmann
d83feb5459 Fix typo in ALA_C.frg file 2009-07-14 22:46:03 +00:00
Kurt Glaesmann
b830fc82ea Add par_all32_lipid.prm & par_all35_ethers.prm 2009-07-02 22:21:18 +00:00
Kurt Glaesmann
3c19e30758 Add some sgm files 2009-07-02 20:51:19 +00:00
Kurt Glaesmann
f3a5fc6903 Add some sgm files 2009-07-02 20:27:42 +00:00
Kurt Glaesmann
7ebe87ff2a fix my mistake in parameter file formatting 2009-07-01 17:17:25 +00:00
Kurt Glaesmann
969501c72e Fix the solvent restart files to be more modern 2009-06-30 23:16:33 +00:00
Kurt Glaesmann
e89cfd84b6 Fix the solvent restart files to be more modern 2009-06-30 21:13:30 +00:00
Kurt Glaesmann
f9bc943d1e Fix comments in fragment files 2009-06-26 22:15:00 +00:00
Kurt Glaesmann
1fca657371 Add the optional ipardef parameter to the segment file 
Does not change any runs, but makes it explicit
 2009-06-26 20:33:58 +00:00
Kurt Glaesmann
0f21598d75 Make sure everything is up to date 2009-06-25 22:10:23 +00:00
Kurt Glaesmann
32f8b66d29 Add newer charmm parameter files. 
Make sure all parameter files have an empty atom type block, so that it is obviously missing
 2009-06-24 17:04:25 +00:00
Kurt Glaesmann
f4cb31be1f Update SPC/E water files to new format and add charmm.par file for the parameters 2009-06-24 17:02:55 +00:00
Kurt Glaesmann
218a2ae117 Add some *.sgm files 2009-06-24 17:01:49 +00:00
Kurt Glaesmann
693ce5adfb Update *.frg files to newer format 2009-06-24 16:59:12 +00:00
Kurt Glaesmann
b06bedb1da NE is neon, not nitrogen version E 2009-06-08 17:38:48 +00:00
d3m299
299e2b16d4 adding fragment file for CCl4 2006-10-05 17:18:07 +00:00
Tjerk Straatsma
3aab6bcc60 Add LCX fragment file 2006-08-08 16:17:42 +00:00
Tjerk Straatsma
8abb4e3fb7 Updated charges for e coli LPS fragments 2006-07-14 18:45:33 +00:00
Tjerk Straatsma
449563a31b Move segments for specific lps molecules into separate sub-directories 2006-03-08 18:54:40 +00:00
Tjerk Straatsma
ec7e8121c4 Terminal fragments for charmm22 2006-02-27 23:51:53 +00:00
Marat Valiev
a7535b728a adding phosphoserine and phosphothreonine residues 2005-01-08 00:43:42 +00:00
Tjerk Straatsma
5aad71bf08 Make all residues a single charge group 2004-12-08 18:53:26 +00:00
Marat Valiev
de8e942b27 fixed incorrect charge group for CZ 2004-11-03 00:24:56 +00:00
Tjerk Straatsma
9f7987927c Fix atom name 2HZ -> 3HZ in neutral Lysine 2004-04-01 17:49:43 +00:00
Tjerk Straatsma
4fcb64d5d6 *** empty log message *** 2004-03-06 03:57:31 +00:00
Tjerk Straatsma
5c8d56b469 Z-matrix definition correction for ARG 2004-02-24 01:43:54 +00:00
Tjerk Straatsma
4221607aeb Ion parameter file 2003-12-18 19:25:52 +00:00
Tjerk Straatsma
e4156427d1 Updated partial charges for solps residues 2003-12-16 02:39:22 +00:00