Reimplement constant acceleration groups

[alexxy/gromacs.git] / src / gromacs / gmxpreprocess / tests / refdata / GetIrTest_HandlesDifferentKindsOfMdpLines.xml

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml
index da5d9ac60bbdf415e4b5adc21627050cf964ec79..f1a0281dc907616ccd7ad911421fb1b300188f3f 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml
+++ b/src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml
@@ -8,7 +8,7 @@
 ; e.g.: -I/home/joe/doe -I/home/mary/roe
 include                  = -I/home/me/stuff
 ; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
-define                   = 
+define                   = -DBOOLVAR -DVAR=VALUE
 
 ; RUN CONTROL PARAMETERS
 integrator               = steep
@@ -20,6 +20,8 @@ nsteps                   = 0
 init_step                = 0
 ; Part index is updated automatically on checkpointing (keeps files separate)
 simulation-part          = 1
+; Multiple time-stepping
+mts                      = no
 ; mode for center of mass motion removal
 comm-mode                = Linear
 ; number of steps for center of mass motion removal
@@ -67,12 +69,10 @@ compressed-x-grps        = System
 energygrps               = 
 
 ; NEIGHBORSEARCHING PARAMETERS
-; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+; cut-off scheme (Verlet: particle based cut-offs)
 cutoff-scheme            = Verlet
 ; nblist update frequency
 nstlist                  = 10
-; ns algorithm (simple or grid)
-ns-type                  = Grid
 ; Periodic boundary conditions: xyz, no, xy
 pbc                      = xyz
 periodic-molecules       = no
@@ -117,31 +117,7 @@ ewald-rtol-lj            = 0.001
 lj-pme-comb-rule         = Geometric
 ewald-geometry           = 3d
 epsilon-surface          = 0
-
-; IMPLICIT SOLVENT ALGORITHM
-implicit-solvent         = No
-
-; GENERALIZED BORN ELECTROSTATICS
-; Algorithm for calculating Born radii
-gb-algorithm             = Still
-; Frequency of calculating the Born radii inside rlist
-nstgbradii               = 1
-; Cutoff for Born radii calculation; the contribution from atoms
-; between rlist and rgbradii is updated every nstlist steps
-rgbradii                 = 1
-; Dielectric coefficient of the implicit solvent
-gb-epsilon-solvent       = 80
-; Salt concentration in M for Generalized Born models
-gb-saltconc              = 0
-; Scaling factors used in the OBC GB model. Default values are OBC(II)
-gb-obc-alpha             = 1
-gb-obc-beta              = 0.8
-gb-obc-gamma             = 4.85
-gb-dielectric-offset     = 0.009
-sa-algorithm             = Ace-approximation
-; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
-; The value -1 will set default value for Still/HCT/OBC GB-models.
-sa-surface-tension       = -1
+implicit-solvent         = no
 
 ; OPTIONS FOR WEAK COUPLING ALGORITHMS
 ; Temperature coupling  
@@ -167,31 +143,8 @@ refcoord-scaling         = No
 
 ; OPTIONS FOR QMMM calculations
 QMMM                     = no
-; Groups treated Quantum Mechanically
+; Groups treated with MiMiC
 QMMM-grps                = 
-; QM method             
-QMmethod                 = 
-; QMMM scheme           
-QMMMscheme               = normal
-; QM basisset           
-QMbasis                  = 
-; QM charge             
-QMcharge                 = 
-; QM multiplicity       
-QMmult                   = 
-; Surface Hopping       
-SH                       = 
-; CAS space options     
-CASorbitals              = 
-CASelectrons             = 
-SAon                     = 
-SAoff                    = 
-SAsteps                  = 
-; Scale factor for MM charges
-MMChargeScaleFactor      = 1
-; Optimization of QM subsystem
-bOPT                     = 
-bTS                      = 
 
 ; SIMULATED ANNEALING  
 ; Type of annealing for each temperature group (no/single/periodic)
@@ -246,6 +199,9 @@ wall-ewald-zfac          = 3
 ; COM PULLING          
 pull                     = no
 
+; AWH biasing          
+awh                      = no
+
 ; ENFORCED ROTATION    
 ; Enforced rotation: No or Yes
 rotation                 = no
@@ -293,11 +249,15 @@ temperature-lambdas      =
 calc-lambda-neighbors    = 1
 init-lambda-weights      = 
 dhdl-print-energy        = no
+sc-function              = beutler
 sc-alpha                 = 0
 sc-power                 = 1
 sc-r-power               = 6
 sc-sigma                 = 0.3
 sc-coul                  = no
+sc-gapsys-scale-linpoint-lj = 0.85
+sc-gapsys-scale-linpoint-q = 0.3
+sc-gapsys-sigma-lj       = 0.3
 separate-dhdl-file       = yes
 dhdl-derivatives         = yes
 dh_hist_size             = 0
@@ -333,5 +293,19 @@ userreal1                = 0
 userreal2                = 0
 userreal3                = 0
 userreal4                = 0
+; Electric fields
+; Format for electric-field-x, etc. is: four real variables:
+; amplitude (V/nm), frequency omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Omega = 0 means static field,
+; sigma = 0 means no pulse, leaving the field to be a cosine function.
+electric-field-x         = 0 0 0 0
+electric-field-y         = 0 0 0 0
+electric-field-z         = 0 0 0 0
+
+; Density guided simulation
+density-guided-simulation-active = false
+
+; QM/MM with CP2K
+qmmm-cp2k-active         = false
 </String>
 </ReferenceData>