--- "GMX2019\\do_x3dna.cpp"	2018-12-13 19:06:05.000000000 +0300
+++ "GMX2016\\do_x3dna.cpp"	2021-02-07 23:08:52.595919100 +0300
@@ -68,6 +68,12 @@
 #include "../ExtractData.h"
 #include "do_x3dna.h"
 
+#if GMX_NATIVE_WINDOWS
+#define NULL_DEVICE  "nul"
+#else
+#define NULL_DEVICE  "/dev/null"
+#endif
+
 void CopyRightMsg() {
 
     const char *copyright[] = {
@@ -1449,17 +1455,17 @@
   dptr=getenv("X3DNA");
   if (!gmx_fexist(dptr))
 	  gmx_fatal(FARGS,"$X3DNA environment not found", dptr);
-  sprintf(find_pair_cmd,"$X3DNA/bin/find_pair %s %s %s",pdbfile, inpfile, bVerbose?"":"2> /dev/null");
+  sprintf(find_pair_cmd,"%s/bin/find_pair %s %s %s", dptr, pdbfile, inpfile, bVerbose?"":"2> " NULL_DEVICE );
   if (bVerbose)
 	  fprintf(stderr,"find_pair command='%s'\n",find_pair_cmd);
 
   //Creating variable for executing command of analyze from X3DNA
   if (bAnalyzeC_Option)
-    sprintf(analyze_cmd,"$X3DNA/bin/analyze -c %s %s", inpfile,bVerbose?"":"2> /dev/null");
+    sprintf(analyze_cmd,"%s/bin/analyze -c %s %s", dptr, inpfile,bVerbose?"":"2> " NULL_DEVICE);
   else
-    sprintf(analyze_cmd,"$X3DNA/bin/analyze %s %s", inpfile,bVerbose?"":"2> /dev/null");
+    sprintf(analyze_cmd,"%s/bin/analyze %s %s", dptr, inpfile,bVerbose?"":"2> " NULL_DEVICE);
   if (bVerbose)
-	  fprintf(stderr,"find_pair command='%s'\n",analyze_cmd);
+	  fprintf(stderr,"analyze command='%s'\n",analyze_cmd);
 
   //Reading first frame
   natoms=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
@@ -1473,8 +1479,10 @@
 
     // Translate the frame to origin, fit (by rotating) it to reference structure
     // and translate again the frame to original position of reference structure
-    reset_x(nfit,ifit,top.atoms.nr,NULL,x,w_rls);
-    do_fit(natoms,w_rls,xref,x);
+   // reset_x(nfit,ifit,top.atoms.nr,NULL,x,w_rls);
+	reset_x(nfit, ifit, natoms, NULL, x, w_rls);
+	
+	do_fit(natoms,w_rls,xref,x);
     for (i = 0; (i < natoms); i++)
          rvec_inc(x[i], x_shift);
   }
@@ -1554,33 +1562,39 @@
   //***************************************************************************************
   //START of Trajectory loop
   //***************************************************************************************
-  do 	{
-	  gmx_rmpbc(gpbc,natoms,box,x);
+  do {
+	  gmx_rmpbc(gpbc, natoms, box, x);
 
 	  //Fitting the frame to reference structure
-	  if (bFit)	{
-      // Translate the frame to origin, fit (by rotating) it to reference structure
-      // and translate again the frame to original position of reference structure
-      reset_x(nfit,ifit,top.atoms.nr,NULL,x,w_rls);
-      do_fit(natoms,w_rls,xref,x);
-      for (i = 0; (i < natoms); i++)
-           rvec_inc(x[i], x_shift);
+	  if (bFit) {
+		  // Translate the frame to origin, fit (by rotating) it to reference structure
+		  // and translate again the frame to original position of reference structure
+	   //   reset_x(nfit,ifit,top.atoms.nr,NULL,x,w_rls);
+		  reset_x(nfit, ifit, natoms, NULL, x, w_rls);
+		  do_fit(natoms, w_rls, xref, x);
+		  for (i = 0; (i < natoms); i++)
+			  rvec_inc(x[i], x_shift);
 	  }
 
 	  //tapein=gmx_ffopen(pdbfile,"w");
 	  //write_pdbfile_indexed(tapein,NULL,atoms,x,ePBC,box,' ',-1,gnx,index,NULL,TRUE);
-      write_sto_conf_indexed(pdbfile, nullptr, &top.atoms, x, nullptr, ePBC, box, gnx, index);
+	  write_sto_conf_indexed(pdbfile, nullptr, &top.atoms, x, nullptr, ePBC, box, gnx, index);
 	  //gmx_ffclose(tapein);
 
 	  //Executing program $X3DNA/bin/find_pair
-	  if(!bRef)
-		  if(0 != system(find_pair_cmd))
-			  gmx_fatal(FARGS,"Failed to execute command: %s",find_pair_cmd);
-
+	  if (!bRef) {
+		   int i;
+		   for (i = 0; i < 3 && 0 != system(find_pair_cmd); ++i);
+           if ( i>=3 )
+ 		       gmx_fatal(FARGS, "Failed to execute command: %s", find_pair_cmd);
+        }
 	  //Executing program $X3DNA/bin/analyze
-	  if(0 != system(analyze_cmd))
-		  gmx_fatal(FARGS,"Failed to execute command: %s",analyze_cmd);
-
+	  {
+		  int i;
+		  for (i = 0; i < 3 && 0 != system(analyze_cmd); ++i);
+		  if (i >= 3)
+		    gmx_fatal(FARGS, "Failed to execute command: %s", analyze_cmd);
+	  }
 	  write_time(t, f_cum_data);
 	  num_bp = add_data_to_files(x3dna_out_file, f_cum_data);
 	  fprintf(fnum_bp,"%12.7f   %d \n",t, num_bp);