Merge branch 'AFM' into multichain

diff --cc source/unres/src_MD-M/chainbuild.F
Simple merge

diff --cc source/unres/src_MD-M/energy_p_new_barrier.F
index 439fb81,2208b17..3192819
--- 1/source/unres/src_MD-M/energy_p_new_barrier.F
--- 2/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@@ -3063,19 -3282,14 +3282,21 @@@ C Loop over i,i+2 and i,i+3 pairs of th
  C
  C 14/01/2014 TURN3,TUNR4 does no go under periodic boundry condition
        do i=iturn3_start,iturn3_end
+         if (i.le.1) cycle
+ C        write(iout,*) "tu jest i",i
          if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
 +C changes suggested by Ana to avoid out of bounds
 +     & .or.((i+4).gt.nres)
 +     & .or.((i-1).le.0)
 +C end of changes by Ana
       &  .or. itype(i+2).eq.ntyp1
 -     &  .or. itype(i+3).eq.ntyp1
 -     &  .or. itype(i-1).eq.ntyp1
 -     &  .or. itype(i+4).eq.ntyp1
 -     &  ) cycle
 +     &  .or. itype(i+3).eq.ntyp1) cycle
 +        if(i.gt.1)then
 +          if(itype(i-1).eq.ntyp1)cycle
 +        end if
 +        if(i.LT.nres-3)then
 +          if (itype(i+4).eq.ntyp1) cycle
 +        end if
          dxi=dc(1,i)
          dyi=dc(2,i)
          dzi=dc(3,i)
@@@ -3097,11 -3311,8 +3318,12 @@@
          num_cont_hb(i)=num_conti
        enddo
        do i=iturn4_start,iturn4_end
+         if (i.le.1) cycle
          if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
 +C changes suggested by Ana to avoid out of bounds
 +     & .or.((i+5).gt.nres)
 +     & .or.((i-1).le.0)
 +C end of changes suggested by Ana
       &    .or. itype(i+3).eq.ntyp1
       &    .or. itype(i+4).eq.ntyp1
       &    .or. itype(i+5).eq.ntyp1
@@@ -3164,11 -3375,8 +3386,12 @@@
  c Loop over all pairs of interacting peptide groups except i,i+2 and i,i+3
  c
        do i=iatel_s,iatel_e
+         if (i.le.1) cycle
          if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
 +C changes suggested by Ana to avoid out of bounds
 +     & .or.((i+2).gt.nres)
 +     & .or.((i-1).le.0)
 +C end of changes by Ana
       &  .or. itype(i+2).eq.ntyp1
       &  .or. itype(i-1).eq.ntyp1
       &                ) cycle
@@@ -3220,12 -3428,9 +3443,13 @@@ c        endi
  c        write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
          num_conti=num_cont_hb(i)
          do j=ielstart(i),ielend(i)
- c          write (iout,*) i,j,itype(i),itype(j)
+ C          write (iout,*) i,j
+          if (j.le.1) cycle
            if (itype(j).eq.ntyp1.or. itype(j+1).eq.ntyp1
 +C changes suggested by Ana to avoid out of bounds
 +     & .or.((j+2).gt.nres)
 +     & .or.((j-1).le.0)
 +C end of changes by Ana
       & .or.itype(j+2).eq.ntyp1
       & .or.itype(j-1).eq.ntyp1
       &) cycle