diff --git a/user-doc/tutorials/belfast-9a/system/mdout.mdp b/user-doc/tutorials/belfast-9a/system/mdout.mdp index f7a0b3a2db962a087ff5d36b53bd2def047d85f8..764812dfae2a0942e8ff11b573fe687eb227f713 100644 --- a/user-doc/tutorials/belfast-9a/system/mdout.mdp +++ b/user-doc/tutorials/belfast-9a/system/mdout.mdp @@ -1,8 +1,8 @@ ; ; File 'mdout.mdp' was generated ; By user: carlo (501) -; On host: Carlos-MacBook-Pro.local -; At date: Thu May 29 23:17:49 2014 +; On host: Carlos-MBP.fritz.box +; At date: Sun Oct 16 17:33:14 2016 ; ; VARIOUS PREPROCESSING OPTIONS @@ -59,16 +59,17 @@ nstlog = 10000 nstcalcenergy = -1 nstenergy = 1000 ; Output frequency and precision for .xtc file -nstxtcout = 10 -xtc-precision = 1000 -; This selects the subset of atoms for the .xtc file. You can -; select multiple groups. By default all atoms will be written. -xtc-grps = protein +nstxout-compressed = 10 +compressed-x-precision = 1000 +; This selects the subset of atoms for the compressed +; trajectory file. You can select multiple groups. By +; default, all atoms will be written. +compressed-x-grps = protein ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS -; cut-off scheme (group: using charge groups, Verlet: particle based cut-offs) +; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups) cutoff-scheme = Verlet ; nblist update frequency nstlist = 10 @@ -77,9 +78,9 @@ ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no -; Allowed energy drift due to the Verlet buffer in kJ/mol/ps per atom, +; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom, ; a value of -1 means: use rlist -verlet-buffer-drift = 0.0001 +verlet-buffer-tolerance = 0.0001 ; nblist cut-off rlist = 0.9 ; long-range cut-off for switched potentials @@ -116,9 +117,10 @@ fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 +ewald-rtol-lj = 0.001 +lj-pme-comb-rule = Geometric ewald_geometry = 3d epsilon_surface = 0 -optimize_fft = yes ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = No @@ -221,7 +223,7 @@ Shake-SOR = no ; Relative tolerance of shake shake-tol = 0.0001 ; Highest order in the expansion of the constraint coupling matrix -lincs-order = 4 +lincs-order = 6 ; Number of iterations in the final step of LINCS. 1 is fine for ; normal simulations, but use 2 to conserve energy in NVE runs. ; For energy minimization with constraints it should be 4 to 8. @@ -253,6 +255,9 @@ pull = no ; Enforced rotation: No or Yes rotation = no +; Group to display and/or manipulate in interactive MD session +IMD-group = + ; NMR refinement stuff ; Distance restraints type: No, Simple or Ensemble disre = No @@ -321,12 +326,19 @@ sim-temp-high = 300 ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = +; Time dependent (pulsed) electric field. Format is omega, time for pulse +; peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving +; the field to be a cosine function. E-xt = E-y = E-yt = E-z = E-zt = +; Ion/water position swapping for computational electrophysiology setups +; Swap positions along direction: no, X, Y, Z +swapcoords = no + ; AdResS parameters adress = no diff --git a/user-doc/tutorials/belfast-9a/system/topol.tpr b/user-doc/tutorials/belfast-9a/system/topol.tpr index cb18503c191b24a9ed533e152407f13bd1c505ae..70e14b9c48f0db1b01a98d5dbdb0b81149c45d96 100644 Binary files a/user-doc/tutorials/belfast-9a/system/topol.tpr and b/user-doc/tutorials/belfast-9a/system/topol.tpr differ