diff --git a/RBBGCMuso/R/calibMuso.R b/RBBGCMuso/R/calibMuso.R
index 2612fbd..400c5e8 100644
--- a/RBBGCMuso/R/calibMuso.R
+++ b/RBBGCMuso/R/calibMuso.R
@@ -105,14 +105,14 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
 
     toModif<-c(epc[2],iniInput[2])
 
-    if(!modifyOriginal & (!is.null(parameters) | !is.null(outVars)))
-    {
+    # if(!modifyOriginal & (!is.null(parameters) | !is.null(outVars)))
+    # {
         
         toModif <- sapply(toModif, function (x){
             paste0(tools::file_path_sans_ext(basename(x)),"-tmp.",tools::file_ext(x))
         })
         
-    }
+    # }
     
     ##change the epc file if and only if there are given parameters
     if(!is.null(parameters)){
@@ -138,6 +138,7 @@ calibMuso <- function(settings=NULL, calibrationPar=NULL,
         writeLines(tmp,iniInput[2])
         rm(list=c("tmp","tmpInd"))
     }
+
     if(!is.null(outVars)){
         outputVarChanges <- putOutVars(iniInput[2], outputVars = outVars, modifyOriginal = !modifyOriginal)
         settings$outputVars[[1]]<-outputVarChanges[[1]]
diff --git a/RBBGCMuso/R/calibration.R b/RBBGCMuso/R/calibration.R
index 105cc58..460ae3e 100644
--- a/RBBGCMuso/R/calibration.R
+++ b/RBBGCMuso/R/calibration.R
@@ -37,6 +37,7 @@ optiMuso <- function(measuredData, parameters = NULL, startDate = NULL,
                      skipSpinup = TRUE,
                      constrains = NULL,
                      plotName = "calib.jpg",
+                     modifyOriginal=TRUE,
 		     likelihood = function(x, y){
 			 exp(-sqrt(mean((x-y)^2)))
 		     },
@@ -115,7 +116,7 @@ optiMuso <- function(measuredData, parameters = NULL, startDate = NULL,
 
     modellOut <- numeric(iterations + 1) # single variable solution
     rmse <- numeric(iterations + 1)
-    origModellOut <- calibMuso(settings=settings,silent=TRUE, skipSpinup = skipSpinup,postProcString=postProcString)
+    origModellOut <- calibMuso(settings=settings,silent=TRUE, skipSpinup = skipSpinup,postProcString=postProcString, modifyOriginal=modifyOriginal)
 
 
     write.csv(x=origModellOut, file=paste0(pretag,1,".csv"))
@@ -138,7 +139,7 @@ optiMuso <- function(measuredData, parameters = NULL, startDate = NULL,
         tmp <- tryCatch(calibMuso(settings = settings,
                                   parameters = randValues[(i-1),],
                                   silent= TRUE,
-                                  skipSpinup = skipSpinup, postProcString = postProcString)[modIndex,colNumb], error = function (e) NULL        )
+                                  skipSpinup = skipSpinup, modifyOriginal=modifyOriginal, postProcString = postProcString)[modIndex,colNumb], error = function (e) NULL        )
         if(is.null(tmp)){
            tmp <- rmse[i] <- modellOut[i] <- NA
         } else {
diff --git a/RBBGCMuso/R/changeMuso.R b/RBBGCMuso/R/changeMuso.R
index d772223..3fa59d1 100644
--- a/RBBGCMuso/R/changeMuso.R
+++ b/RBBGCMuso/R/changeMuso.R
@@ -33,6 +33,10 @@ changemulline <- function(filePaths, calibrationPar, contents, fileOut, fileToCh
         changeMusoC(inFile = filePaths[selectFileToWrite(filePaths, fileToChange)],
                     outFile = fileOut[selectFileToWrite(filePaths, fileToChange)],
                     parMat)
+        if(modifyOriginal){
+             # browser()
+            file.copy(fileOut[selectFileToWrite(filePaths, fileToChange)],filePaths[selectFileToWrite(filePaths, fileToChange)],overwrite = TRUE)
+        }
     }
     
     if(fileToChange == "both"){