********>Bugfix 26:
Author: Ross Walker
Date: 11/23/2004

Programs: sander.QMMM

Description: The velocity array is not correctly allocated for simulations
             involving link atoms. This means that QMMM simulations involving
             link atoms may be unstable.

Fix:  apply the following patch to amber8/src/sander/locmem.f
                                   amber8/test/qmmm/divcon/crambin_md.out.save

------------------------------------------------------------------------------
--- src/sander/locmem.f	2004-11-23 20:05:44.000000000 -0800
+++ src/sander/locmem.f	2004-11-23 20:06:15.000000000 -0800
@@ -179,10 +179,10 @@
    call adj_mem_ptr( r_ptr, lcrd, 3*natom + mxvar+3*ncpp )
    call adj_mem_ptr( r_ptr, lforce, 3*natom + mxvar + 40+3*ncpp )
    if (imin == 0) then
-      call adj_mem_ptr( r_ptr, lvel,  3*natom + mxvar )
-      call adj_mem_ptr( r_ptr, lvel2, 3*natom + mxvar )
+      call adj_mem_ptr( r_ptr, lvel,  3*natom + mxvar + 3*ncpp)
+      call adj_mem_ptr( r_ptr, lvel2, 3*natom + mxvar + 3*ncpp)
    else
-      call adj_mem_ptr( r_ptr, lvel, 6*(3*natom + mxvar) )
+      call adj_mem_ptr( r_ptr, lvel, 6*(3*natom + mxvar + 3*ncpp) )
       call adj_mem_ptr( r_ptr, lvel2, 0 )
    end if
    call adj_mem_ptr( r_ptr, l45, 3*natom + mxvar+3*ncpp )

------------------------------------------------------------------

--- test/qmmm/divcon/crambin_md.out.save	2004-08-08 10:31:03.000000000 -0700
+++ test/qmmm/divcon/crambin_md.out.save	2004-11-23 20:09:14.000000000 -0800
@@ -3,7 +3,7 @@
           Amber 8  SANDER                 Scripps/UCSF 2004
           -------------------------------------------------------
 
-| Run on 06/18/2004 at 11:32:49
+| Run on 11/23/2004 at 20:08:39
   [-O]verwriting output
 
 File Assignments:
@@ -60,13 +60,13 @@
 
 
 |     Memory Use     Allocated
-|     Real               18266
+|     Real               20066
 |     Hollerith           5400
 |     Integer            55343
 |     Max Pairs         205761
 |     Max Rstack         56420
 |     Max Istack          3210
-|       Total             1637 kbytes
+|       Total             1651 kbytes
 | Duplicated    0 dihedrals
 | Duplicated    0 dihedrals
 
@@ -124,8 +124,8 @@
  ------------------------------------------------------------------------------
 
 
- NSTEP =        1   TIME(PS) =       0.001  TEMP(K) =     0.02  PRESS =     0.0
- Etot   =      -856.0018  EKtot   =         0.0332  EPtot      =      -856.0350
+ NSTEP =        1   TIME(PS) =       0.001  TEMP(K) =     0.01  PRESS =     0.0
+ Etot   =      -856.0253  EKtot   =         0.0097  EPtot      =      -856.0350
  BOND   =        24.6793  ANGLE   =        75.7358  DIHED      =       173.5178
  1-4 NB =       172.5680  1-4 EEL =      2309.5141  VDWAALS    =      -271.4044
  EELEC  =     -3215.6062  EHBOND  =         0.0000  RESTRAINT  =         0.0000
@@ -134,108 +134,108 @@
 
 
  NSTEP =        2   TIME(PS) =       0.002  TEMP(K) =     2.11  PRESS =     0.0
- Etot   =      -856.2042  EKtot   =         4.0775  EPtot      =      -860.2818
+ Etot   =      -856.2092  EKtot   =         4.0782  EPtot      =      -860.2874
  BOND   =        23.1250  ANGLE   =        74.9422  DIHED      =       173.4796
  1-4 NB =       172.4272  1-4 EEL =      2309.3410  VDWAALS    =      -271.5589
  EELEC  =     -3215.6356  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -126.4023
+ ESCF   =      -126.4079
  ------------------------------------------------------------------------------
 
 
  NSTEP =        3   TIME(PS) =       0.003  TEMP(K) =     7.08  PRESS =     0.0
- Etot   =      -856.6141  EKtot   =        13.6684  EPtot      =      -870.2825
- BOND   =        19.5732  ANGLE   =        72.8004  DIHED      =       173.3731
- 1-4 NB =       172.0315  1-4 EEL =      2308.8151  VDWAALS    =      -272.0158
+ Etot   =      -856.6127  EKtot   =        13.6847  EPtot      =      -870.2974
+ BOND   =        19.5733  ANGLE   =        72.8005  DIHED      =       173.3731
+ 1-4 NB =       172.0314  1-4 EEL =      2308.8151  VDWAALS    =      -272.0157
  EELEC  =     -3215.6774  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -129.1827
+ ESCF   =      -129.1977
  ------------------------------------------------------------------------------
 
 
- NSTEP =        4   TIME(PS) =       0.004  TEMP(K) =    12.38  PRESS =     0.0
- Etot   =      -856.7865  EKtot   =        23.9086  EPtot      =      -880.6951
- BOND   =        16.2311  ANGLE   =        69.9499  DIHED      =       173.2208
- 1-4 NB =       171.4524  1-4 EEL =      2307.9223  VDWAALS    =      -272.7610
+ NSTEP =        4   TIME(PS) =       0.004  TEMP(K) =    12.39  PRESS =     0.0
+ Etot   =      -856.7816  EKtot   =        23.9369  EPtot      =      -880.7185
+ BOND   =        16.2314  ANGLE   =        69.9502  DIHED      =       173.2208
+ 1-4 NB =       171.4518  1-4 EEL =      2307.9223  VDWAALS    =      -272.7607
  EELEC  =     -3215.6122  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -131.0984
+ ESCF   =      -131.1221
  ------------------------------------------------------------------------------
 
 
- NSTEP =        5   TIME(PS) =       0.005  TEMP(K) =    16.71  PRESS =     0.0
- Etot   =      -856.6969  EKtot   =        32.2717  EPtot      =      -888.9686
- BOND   =        14.3432  ANGLE   =        67.2341  DIHED      =       173.0568
- 1-4 NB =       170.7833  1-4 EEL =      2306.6563  VDWAALS    =      -273.7785
- EELEC  =     -3215.3021  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -131.9616
+ NSTEP =        5   TIME(PS) =       0.005  TEMP(K) =    16.73  PRESS =     0.0
+ Etot   =      -856.6956  EKtot   =        32.3137  EPtot      =      -889.0093
+ BOND   =        14.3439  ANGLE   =        67.2348  DIHED      =       173.0568
+ 1-4 NB =       170.7816  1-4 EEL =      2306.6563  VDWAALS    =      -273.7779
+ EELEC  =     -3215.3022  EHBOND  =         0.0000  RESTRAINT  =         0.0000
+ ESCF   =      -132.0026
  ------------------------------------------------------------------------------
 
 
- NSTEP =        6   TIME(PS) =       0.006  TEMP(K) =    20.45  PRESS =     0.0
- Etot   =      -856.6346  EKtot   =        39.5051  EPtot      =      -896.1397
- BOND   =        13.5235  ANGLE   =        65.4564  DIHED      =       172.9226
- 1-4 NB =       170.1118  1-4 EEL =      2305.0366  VDWAALS    =      -275.0414
- EELEC  =     -3214.6582  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -133.4909
+ NSTEP =        6   TIME(PS) =       0.006  TEMP(K) =    20.48  PRESS =     0.0
+ Etot   =      -856.6510  EKtot   =        39.5631  EPtot      =      -896.2142
+ BOND   =        13.5246  ANGLE   =        65.4577  DIHED      =       172.9226
+ 1-4 NB =       170.1081  1-4 EEL =      2305.0366  VDWAALS    =      -275.0403
+ EELEC  =     -3214.6583  EHBOND  =         0.0000  RESTRAINT  =         0.0000
+ ESCF   =      -133.5653
  ------------------------------------------------------------------------------
 
 
- NSTEP =        7   TIME(PS) =       0.007  TEMP(K) =    23.82  PRESS =     0.0
- Etot   =      -856.7552  EKtot   =        46.0168  EPtot      =      -902.7720
- BOND   =        12.9629  ANGLE   =        65.1670  DIHED      =       172.8628
- 1-4 NB =       169.4956  1-4 EEL =      2303.1223  VDWAALS    =      -276.4925
+ NSTEP =        7   TIME(PS) =       0.007  TEMP(K) =    23.86  PRESS =     0.0
+ Etot   =      -856.7998  EKtot   =        46.0895  EPtot      =      -902.8893
+ BOND   =        12.9645  ANGLE   =        65.1688  DIHED      =       172.8630
+ 1-4 NB =       169.4894  1-4 EEL =      2303.1224  VDWAALS    =      -276.4911
  EELEC  =     -3213.6938  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -136.1965
+ ESCF   =      -136.3125
  ------------------------------------------------------------------------------
 
 
- NSTEP =        8   TIME(PS) =       0.008  TEMP(K) =    25.85  PRESS =     0.0
- Etot   =      -856.8532  EKtot   =        49.9354  EPtot      =      -906.7886
- BOND   =        12.7530  ANGLE   =        66.5323  DIHED      =       172.9210
- 1-4 NB =       168.9480  1-4 EEL =      2301.0153  VDWAALS    =      -278.0396
+ NSTEP =        8   TIME(PS) =       0.008  TEMP(K) =    25.90  PRESS =     0.0
+ Etot   =      -856.9223  EKtot   =        50.0189  EPtot      =      -906.9412
+ BOND   =        12.7550  ANGLE   =        66.5343  DIHED      =       172.9212
+ 1-4 NB =       168.9389  1-4 EEL =      2301.0154  VDWAALS    =      -278.0384
  EELEC  =     -3212.5404  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -138.3781
+ ESCF   =      -138.5271
  ------------------------------------------------------------------------------
 
 
- NSTEP =        9   TIME(PS) =       0.009  TEMP(K) =    25.73  PRESS =     0.0
- Etot   =      -856.7500  EKtot   =        49.6986  EPtot      =      -906.4487
- BOND   =        13.6697  ANGLE   =        69.3071  DIHED      =       173.1346
- 1-4 NB =       168.4346  1-4 EEL =      2298.8499  VDWAALS    =      -279.5746
- EELEC  =     -3211.4175  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -138.8523
+ NSTEP =        9   TIME(PS) =       0.009  TEMP(K) =    25.78  PRESS =     0.0
+ Etot   =      -856.8300  EKtot   =        49.7917  EPtot      =      -906.6217
+ BOND   =        13.6716  ANGLE   =        69.3091  DIHED      =       173.1348
+ 1-4 NB =       168.4229  1-4 EEL =      2298.8500  VDWAALS    =      -279.5744
+ EELEC  =     -3211.4174  EHBOND  =         0.0000  RESTRAINT  =         0.0000
+ ESCF   =      -139.0184
  ------------------------------------------------------------------------------
 
 
- NSTEP =       10   TIME(PS) =       0.010  TEMP(K) =    24.15  PRESS =     0.0
- Etot   =      -856.5124  EKtot   =        46.6529  EPtot      =      -903.1653
- BOND   =        15.8617  ANGLE   =        72.9092  DIHED      =       173.5310
- 1-4 NB =       167.8825  1-4 EEL =      2296.7703  VDWAALS    =      -281.0031
- EELEC  =     -3210.5663  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -138.5507
+ NSTEP =       10   TIME(PS) =       0.010  TEMP(K) =    24.21  PRESS =     0.0
+ Etot   =      -856.5935  EKtot   =        46.7574  EPtot      =      -903.3510
+ BOND   =        15.8628  ANGLE   =        72.9116  DIHED      =       173.5312
+ 1-4 NB =       167.8692  1-4 EEL =      2296.7706  VDWAALS    =      -281.0047
+ EELEC  =     -3210.5660  EHBOND  =         0.0000  RESTRAINT  =         0.0000
+ ESCF   =      -138.7257
  ------------------------------------------------------------------------------
 
 
       A V E R A G E S   O V E R      10 S T E P S
 
 
- NSTEP =       10   TIME(PS) =       0.010  TEMP(K) =    15.83  PRESS =     0.0
- Etot   =      -856.5809  EKtot   =        30.5768  EPtot      =      -887.1577
- BOND   =        16.6722  ANGLE   =        70.0034  DIHED      =       173.2020
- 1-4 NB =       170.4135  1-4 EEL =      2304.7043  VDWAALS    =      -275.1670
- EELEC  =     -3214.0710  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =      -132.9153
+ NSTEP =       10   TIME(PS) =       0.010  TEMP(K) =    15.85  PRESS =     0.0
+ Etot   =      -856.6121  EKtot   =        30.6244  EPtot      =      -887.2365
+ BOND   =        16.6731  ANGLE   =        70.0045  DIHED      =       173.2021
+ 1-4 NB =       170.4088  1-4 EEL =      2304.7044  VDWAALS    =      -275.1666
+ EELEC  =     -3214.0709  EHBOND  =         0.0000  RESTRAINT  =         0.0000
+ ESCF   =      -132.9919
  ------------------------------------------------------------------------------
 
 
       R M S  F L U C T U A T I O N S
 
 
- NSTEP =       10   TIME(PS) =       0.010  TEMP(K) =     9.38  PRESS =     0.0
- Etot   =         0.2598  EKtot   =        18.1254  EPtot      =        18.3276
- BOND   =         4.1048  ANGLE   =         3.7120  DIHED      =         0.2475
- 1-4 NB =         1.6104  1-4 EEL =         4.3490  VDWAALS    =         3.2914
- EELEC  =         1.8284  EHBOND  =         0.0000  RESTRAINT  =         0.0000
- ESCF   =         4.8014
-|E(PBS) =         0.0346
+ NSTEP =       10   TIME(PS) =       0.010  TEMP(K) =     9.40  PRESS =     0.0
+ Etot   =         0.2689  EKtot   =        18.1642  EPtot      =        18.3894
+ BOND   =         4.1042  ANGLE   =         3.7115  DIHED      =         0.2474
+ 1-4 NB =         1.6151  1-4 EEL =         4.3490  VDWAALS    =         3.2916
+ EELEC  =         1.8285  EHBOND  =         0.0000  RESTRAINT  =         0.0000
+ ESCF   =         4.8647
+|E(PBS) =         0.0256
  ------------------------------------------------------------------------------
 
 
@@ -243,20 +243,20 @@
    5.  TIMINGS
 --------------------------------------------------------------------------------
 
-|    Read coords time           0.01 ( 0.02% of Total)
-|          Nonbond force              0.11 ( 0.26% of Force)
-|          QMMM energy               41.20 (99.68% of Force)
-|          Bond/Angle/Dihedral        0.02 ( 0.06% of Force)
-|       Force time                41.33 (99.59% of Runmd)
-|       Verlet update time         0.16 ( 0.39% of Runmd)
+|    Read coords time           0.00 ( 0.01% of Total)
+|          Nonbond force              0.13 ( 0.38% of Force)
+|          QMMM energy               34.83 (99.52% of Force)
+|          Bond/Angle/Dihedral        0.04 ( 0.10% of Force)
+|       Force time                35.00 (99.43% of Runmd)
+|       Verlet update time         0.19 ( 0.54% of Runmd)
 |       Other                      0.01 ( 0.03% of Runmd)
-|    Runmd Time                41.50 (99.86% of Total)
-|    Other                      0.05 ( 0.12% of Total)
-| Total time                41.56 (100.0% of ALL  )
+|    Runmd Time                35.20 (99.88% of Total)
+|    Other                      0.04 ( 0.11% of Total)
+| Total time                35.24 (100.0% of ALL  )
 
 | Highest rstack allocated:          0
 | Highest istack allocated:          0
-|           Job began  at 11:32:49.556  on 06/18/2004
-|           Setup done at 11:32:49.616  on 06/18/2004
-|           Run   done at 11:33:31.120  on 06/18/2004
+|           Job began  at 20:08:39.203  on 11/23/2004
+|           Setup done at 20:08:39.245  on 11/23/2004
+|           Run   done at 20:09:14.448  on 11/23/2004
 |     wallclock() was called     434 times

----------------------------------------------------------------------------
Temporary workaround: NONE