********>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