started reformating

Author: simongravelle

tutorial1/ff/forcefield.itp

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+[ defaults ]
+; nbfunc  comb-rule  gen-pairs  fudgeLJ  fudgeQQ
+  1       2          no         1.0      0.833
+
+[ atomtypes ]
+; name  at.num  mass      charge  ptype  sigma    epsilon
+  Na    11      22.9900   1.0000  A      0.23100  0.45000
+  OS     8      15.9994  -1.0000  A      0.38600  0.12
+  SO    16      32.0600   2.0000  A      0.35500  1.0465
+  HW     1       1.0079   0.5270  A      0.00000  0.00000
+  OW     8      15.9994   0.0000  A      0.31650  0.77323
+  MW     0       0.0000  -1.0540  D      0.00000  0.00000

tutorial1/ff/h2o.itp

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+[ moleculetype ]
+; molname  nrexcl
+  SOL      2
+
+[ atoms ]
+; id  at-type  res-nr  res-name  at-name  cg-nr  charge  mass
+  1   OW	     1       SOL       OW1      1      0.000    15.9994
+  2   HW       1       SOL       HW1      1      0.527     1.0079
+  3   HW       1       SOL       HW2      1      0.527     1.0079
+  4   MW       1       SOL       MW1      1     -1.054     0.0000
+
+[ settles ]
+; i  funct  doh      dhh
+  1  1      0.09572  0.15139
+
+[ virtual_sites3 ]
+; Vsite from          funct        a               b
+4     1     2     3     1       0.089608       0.089608
+
+[ exclusions ]
+1 2 3 4
+2 1 3 4
+3 1 2 4
+4 1 2 3

tutorial1/ff/na.itp

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+[ moleculetype ]
+; molname nrexcl
+  Na      1
+
+[ atoms ]
+; id  at-type  res-nr  res-name  at-name  cg-nr  charge  mass
+  1   Na       1       Na        Na1      1      1.000   22.9900

tutorial1/ff/so4.itp

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+[moleculetype]
+; name  nrexcl
+  SO4   1
+
+[ atoms ]
+; id  at-type  res-nr  res-name  at-name  cg-nr  charge  mass
+  1   OS       1       SO4       O1       1     -1.000   15.9994
+  2   OS       1       SO4       O2       1     -1.000   15.9994
+  3   OS       1       SO4       O3       1     -1.000   15.9994
+  4   OS       1       SO4       O4       1     -1.000   15.9994
+  5   SO       1       SO4       S1       1      2.000   32.0600
+
+[ bonds ]
+;  ai   aj  funct   c0         c1
+    1    5    1   0.1520   3.7656e4
+    2    5    1   0.1520   3.7656e4
+    3    5    1   0.1520   3.7656e4
+    4    5    1   0.1520   3.7656e4
+
+[ angles ]
+;  ai   aj   ak  funct   angle     fc
+    1    5    2    1    109.5  520
+    1    5    3    1    109.5  520
+    1    5    4    1    109.5  520
+    2    5    3    1    109.5  520
+    2    5    4    1    109.5  520
+    3    5    4    1    109.5  520
+    
+[exclusions]
+1       2       3       4       5
+2       1       3       4       5
+3       1       2       4       5
+4       1       2       3       5
+5       1       2       3       4

tutorial1/inputs/min.mdp

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+integrator = steep
+nsteps = 5000
+nstxout = 10

tutorial1/inputs/npt.mdp

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+integrator = md
+nsteps = 80000
+dt = 0.001
+
+comm_mode = linear
+comm_grps = system
+
+cutoff-scheme = Verlet
+nstlist = 10
+ns_type = grid
+
+nstlog = 100
+nstenergy = 100
+nstxout-compressed = 200
+
+vdw-type = Cut-off
+rvdw = 1.0
+
+coulombtype = pme
+fourierspacing = 0.1
+pme-order = 4
+rcoulomb = 1.0
+
+constraint-algorithm = lincs
+constraints = hbonds
+
+tcoupl = v-rescale
+ld-seed = 48456
+tc-grps = Water non-Water
+tau-t = 0.5 0.5
+ref-t = 360 360
+
+pcoupl = C-rescale
+Pcoupltype = isotropic
+tau_p = 1.0
+ref_p = 1.0
+compressibility = 4.5e-5

tutorial1/inputs/nvt-minimalist.mdp

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+integrator = md
+nsteps = 20000
+dt = 0.001
+
+nstlog = 100
+nstenergy = 100
+nstxout-compressed = 200
+
+tcoupl = v-rescale
+ref-t = 360
+tc-grps = system
+tau-t = 0.5

tutorial1/inputs/nvt.mdp

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+integrator = md
+nsteps = 20000
+dt = 0.001
+
+comm_mode = linear
+comm_grps = system
+
+gen-vel = yes
+gen-temp = 360
+
+cutoff-scheme = Verlet
+nstlist = 10
+ns_type = grid
+
+nstlog = 100
+nstenergy = 100
+nstxout-compressed = 200
+
+vdw-type = Cut-off
+rvdw = 1.0
+
+coulombtype = pme
+fourierspacing = 0.1
+pme-order = 4
+rcoulomb = 1.0
+
+constraint-algorithm = lincs
+constraints = hbonds
+
+tcoupl = v-rescale
+ld-seed = 48456
+tc-grps = Water non-Water
+tau-t = 0.5 0.5
+ref-t = 360 360

tutorial1/inputs/production.mdp

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+integrator = md
+nsteps = 400000
+dt = 0.001
+
+comm_mode = linear
+comm_grps = system
+
+cutoff-scheme = Verlet
+nstlist = 10
+ns_type = grid
+
+nstlog = 100
+nstenergy = 100
+nstxout-compressed = 1000
+
+vdw-type = Cut-off
+rvdw = 1.0
+
+coulombtype = pme
+fourierspacing = 0.1
+pme-order = 4
+rcoulomb = 1.0
+
+constraint-algorithm = lincs
+constraints = hbonds
+
+tcoupl = v-rescale
+ld-seed = 48456
+tc-grps = Water non-Water
+tau-t = 0.5 0.5
+ref-t = 360 360

tutorial1/inputs/video.mdp

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+integrator = md
+nsteps = 500
+dt = 0.001
+
+comm_mode = linear
+comm_grps = system
+
+cutoff-scheme = Verlet
+nstlist = 10
+ns_type = grid
+
+nstlog = 100
+nstenergy = 100
+nstxout-compressed = 2
+
+vdw-type = Cut-off
+rvdw = 1.0
+
+coulombtype = pme
+fourierspacing = 0.1
+pme-order = 4
+rcoulomb = 1.0
+
+constraint-algorithm = lincs
+constraints = hbonds
+
+tcoupl = v-rescale
+ld-seed = 48456
+tc-grps = Water non-Water
+tau-t = 0.5 0.5
+ref-t = 360 360