********>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