GROMACS

The first few lines of the "Input parameter" section in the log file show clearly that the formatting/indentation broke slightly:

Input Parameters:                                       
   integrator                     = md                  
   nsteps               = 10000                         
   init-step            = 0                             
   cutoff-scheme                  = Verlet              
   ns-type                        = Grid                
   nstlist              = 20                            
   ndelta               = 2                             
   nstcomm              = 100                           
   comm-mode                      = Linear              
   nstlog               = 5000                          
   nstxout              = 0                             
   nstvout              = 0                             
   nstfout              = 0                             
   nstcalcenergy        = 100                           
   nstenergy            = 500                           
   nstxout-compressed   = 0                             
   init-t               = 0                             
   delta-t              = 0.002                         
   x-compression-precision = 1000                       
   fourierspacing       = 0.12375                       
   nkx                  = 96                            
   nky                  = 96                            
   nkz                  = 96                            
   pme-order            = 4                             
   ewald-rtol           = 0.0001                        
   ewald-rtol-lj        = 0.0001                        
   ewald-geometry       = 0                             
   epsilon-surface      = 0                             
   optimize-fft                   = FALSE               
   lj-pme-comb-rule               = Geometric           
   ePBC                           = xyz                 
   bPeriodicMols                  = FALSE               
   bContinuation                  = FALSE               
   bShakeSOR                      = FALSE               
   etc                            = V-rescale           
   bPrintNHChains                 = FALSE               
   nsttcouple           = 20                            
   epc                            = No                  
   epctype                        = Isotropic           
   nstpcouple           = -1                            
   tau-p                = 1