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miscellaneous maintenance #1

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jmborr opened this issue May 24, 2017 · 0 comments
Open

miscellaneous maintenance #1

jmborr opened this issue May 24, 2017 · 0 comments
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jmborr commented May 24, 2017

This issue is to be permanently opened
@jmborr jmborr self-assigned this May 24, 2017
jmborr added a commit that referenced this issue May 24, 2017
@jmborr
Refs #1 New notebook and gitignore
785b69c
jmborr added a commit that referenced this issue May 26, 2017
@jmborr
Refs #1 Reference in the notebook to the viewer
d71b02b
jmborr added a commit that referenced this issue Jun 5, 2017
@jmborr
Refs #1 Added Panchao info
c1293d9
jmborr added a commit that referenced this issue Jun 5, 2017
@jmborr
Refs #1 Created monomer folder
ffb0158
jmborr added a commit that referenced this issue Jun 5, 2017
@jmborr
Refs #1 gromacs tutorial files
dcc5ad0
jmborr added a commit that referenced this issue Jun 6, 2017
@jmborr
Refs #1 analysis of relax_2 run
a6ecb1d
jmborr added a commit that referenced this issue Jun 6, 2017
@jmborr
Refs #1 Add JPG to gitignore exceptions
1bc948d
jmborr added a commit that referenced this issue Jun 6, 2017
@jmborr
Refs #1 Fix figure sizes
b901b2a
jmborr added a commit that referenced this issue Jun 7, 2017
@jmborr
Refs #1 Increased box size and redo simulation
2da0ab2
jmborr added a commit that referenced this issue Jun 7, 2017
@jmborr
Refs #1 Center protein in the box
96da809
jmborr added a commit that referenced this issue Jun 8, 2017
@jmborr
Refs #1 Find closest water to protein
db86dbe
jmborr added a commit that referenced this issue Jun 9, 2017
@jmborr
Refs #1 Strip waters to 0.17 hydration
a57826f
jmborr added a commit that referenced this issue Jun 12, 2017
@jmborr
Refs #1 References on simulations of silica
074eace
jmborr added a commit that referenced this issue Jun 12, 2017
@jmborr
Refs #1 Fix typo
01a098e
jmborr added a commit that referenced this issue Jun 12, 2017
@jmborr
Refs #1 New reference
fca5047
jmborr added a commit that referenced this issue Jun 13, 2017
@jmborr
Refs #1 Added link to ions mdp
91bb033
jmborr added a commit that referenced this issue Jun 13, 2017
@jmborr
Refs #1 Interface force field seminar
1fecb48
jmborr added a commit that referenced this issue Jun 13, 2017
@jmborr
Refs #1 Heinz slides
14b7fa2
jmborr added a commit that referenced this issue Jun 14, 2017
@jmborr
Refs #1 Added cristobalite
7331fd2
jmborr added a commit that referenced this issue Jun 14, 2017
@jmborr
Refs #1 changed directory for amorphous silica from MD
b401ba7
jmborr added a commit that referenced this issue Jun 15, 2017
@jmborr
Refs #1 Added gro files
d9a0f66
jmborr added a commit that referenced this issue Jun 15, 2017
@jmborr
Refs #1 merge protein and silica in a single PDB file
e4dfd57
jmborr added a commit that referenced this issue Jun 16, 2017
@jmborr
Refs #1 force fields and references for bulk silica
8ead641
jmborr added a commit that referenced this issue Jun 20, 2017
@jmborr
Refs #1 Force fields and carving the protein in cristobalite
6fa45c1
jmborr added a commit that referenced this issue Jun 21, 2017
@jmborr
Refs #1 starting to produce topology for cristobalite
1538d94
jmborr added a commit that referenced this issue Jun 21, 2017
@jmborr
Refs #1 modified bonded file
e12946b
jmborr added a commit that referenced this issue Jun 21, 2017
@jmborr
Refs #1 cristobalite small runs
12a13ac
jmborr added a commit that referenced this issue Jun 22, 2017
@jmborr
Refs #1 relaxing cristobalite_2_2_2
f4e04b6
jmborr added a commit that referenced this issue Jun 22, 2017
@jmborr
Refs #1 checkpoint file
1b54894
jmborr added a commit that referenced this issue Jun 22, 2017
@jmborr
Refs #1 gmx_commands script
75fda38
jmborr added a commit that referenced this issue Jun 22, 2017
@jmborr
Refs #1 plot msd
172d7bb
jmborr added a commit that referenced this issue Jun 23, 2017
@jmborr
Refs #1 directory for cristobalite with no bonds
c0683c6
jmborr added a commit that referenced this issue Jun 23, 2017
@jmborr
Refs #1 topology for nonbonded silica
4b1c7ee
jmborr added a commit that referenced this issue Jun 23, 2017
@jmborr
Refs #1 rename Other2 to Silica
282a151
jmborr added a commit that referenced this issue Jun 23, 2017
@jmborr
Refs #1 minor changes
8e8fd9b
jmborr added a commit that referenced this issue Jun 26, 2017
@jmborr
Refs #1 upload remaining of the force field
f67c64c
jmborr added a commit that referenced this issue Jun 26, 2017
@jmborr
Refs #1 Fixed SIO charge for neutral system
bf117ad
kevinslater added a commit that referenced this issue Jun 28, 2017
@kevinslater
Refs #1 ipython test
31dcf49
jmborr added a commit that referenced this issue Jun 29, 2017
@jmborr
Refs #1 topology for carved cristobalite with bonds
bea5403
kevinslater added a commit that referenced this issue Jun 29, 2017
@kevinslater
Refs #1 added axis labels
47766e0
kevinslater added a commit that referenced this issue Jun 29, 2017
@kevinslater
Refs #1 plot of average MSD
90173e6
kevinslater added a commit that referenced this issue Jun 29, 2017
@kevinslater
Refs #1 simulations of small cristobalite
53807be
kevinslater added a commit that referenced this issue Jun 29, 2017
@kevinslater
Refs #1 applying restraints to the nonbonded system
dbac8bb
jmborr added a commit that referenced this issue Jun 29, 2017
@jmborr
Refs #1 confinedBSA in silica with bonds
4af4b0b
jmborr added a commit that referenced this issue Jun 29, 2017
@jmborr
Refs #1 correct typo in directory name
d8e4d3e
kevinslater added a commit that referenced this issue Jun 30, 2017
@kevinslater
Refs #1 creating nonbonded system restraints
d11320c
kevinslater added a commit that referenced this issue Jun 30, 2017
@kevinslater
Refs #1 topology for nonbonded silica w/ restraints
4840dce
kevinslater added a commit that referenced this issue Jun 30, 2017
@kevinslater
Refs #1 sample job script
50fb217
kevinslater added a commit that referenced this issue Jun 30, 2017
@kevinslater
Refs #1 nonbonded restraints
f9506cd
jmborr added a commit that referenced this issue Jul 3, 2017
@jmborr
Refs #1 Remove wholesytem
d4924e5
jmborr added a commit that referenced this issue Jul 3, 2017
@jmborr
Refs #1 Other systems at diff charge and hidr.
1b82e87
jmborr added a commit that referenced this issue Jul 5, 2017
@jmborr
Refs #1 appeding runs in Titan
e8cd153
jmborr added a commit that referenced this issue Jul 6, 2017
@jmborr
Refs #1 Log equil_1
0733157
jmborr added a commit that referenced this issue Jul 7, 2017
@jmborr
Refs #1 comparing different q_OSI and ovl
7140cf3
jmborr added a commit that referenced this issue Jul 10, 2017
@jmborr
Refs #1 rename certain directories and new h017_q0.90_ovl2.5
7ca3508
jmborr added a commit that referenced this issue Jul 10, 2017
@jmborr
Refs #1 scripts for temperature scan
7b8a82e
jmborr added a commit that referenced this issue Jul 10, 2017
@jmborr
Refs #1 Correct tau_t value
06f4412
jmborr added a commit that referenced this issue Aug 11, 2017
@jmborr
Refs #1 temperature scan
e24e6e5
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