********>Bugfix 38: Author: Gustavo Seabra, University of Florida Date: 09/07/2007 Programs: sander Description: This bugfix resolves the issue with the SMD module in which the program would generate and error if the moving distance was large (around 100 Angstroms). Fix: This patch acctually affects multiple files. Run it from the $AMBERHOME directory, with: $ patch -p0 -N -r patch_rejects < bugfix.36 ------------------------------------------------------------------------------ Created with the command: $ diff -C 5 src/sander/nmr.f_old src/sander/nmr.f ------------------------------------------------------------------------------ *** src/sander/nmr.f 2007-05-07 16:02:27.000000000 -0400 --- src/sander/nmr.f 2007-05-07 16:03:01.000000000 -0400 *************** *** 4006,4017 **** write(6,'(/2x,a)') 'rk2 should not be 0' endif r1=r2-100 r4=r3+100 ! r1a=r1 ! r4a=r4 drjar=(r2a-r2)/(nstep2-nstep1) endif !jar ! Check to make sure maximum allowable number of weight cards not exceeded --- 4006,4017 ---- write(6,'(/2x,a)') 'rk2 should not be 0' endif r1=r2-100 r4=r3+100 ! r1a=r2a-100 ! r4a=r3a+100 drjar=(r2a-r2)/(nstep2-nstep1) endif !jar ! Check to make sure maximum allowable number of weight cards not exceeded *** test/jar/mdout.jar.save_old 2007-08-29 15:28:51.000000000 -0400 --- test/jar/mdout.jar.save 2007-08-29 16:58:36.000000000 -0400 *************** *** 1,11 **** ------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 02/13/2007 at 17:33:44 [-O]verwriting output File Assignments: | MDIN: gbin | MDOUT: mdout.jar --- 1,11 ---- ------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 08/29/2007 at 16:57:21 [-O]verwriting output File Assignments: | MDIN: gbin | MDOUT: mdout.jar *************** *** 41,51 **** -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- ! | Flags: | New format PARM file being parsed. | Version = 1.000 Date = 07/12/01 Time = 15:10:28 NATOM = 640 NTYPES = 14 NBONH = 220 MBONA = 468 NTHETH = 500 MTHETA = 726 NPHIH = 918 MPHIA = 1226 NHPARM = 0 NPARM = 0 NNB = 3568 NRES = 20 --- 41,51 ---- -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- ! | Flags: MPI | New format PARM file being parsed. | Version = 1.000 Date = 07/12/01 Time = 15:10:28 NATOM = 640 NTYPES = 14 NBONH = 220 MBONA = 468 NTHETH = 500 MTHETA = 726 NPHIH = 918 MPHIA = 1226 NHPARM = 0 NPARM = 0 NNB = 3568 NRES = 20 *************** *** 54,70 **** IFBOX = 0 NMXRS = 35 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated ! | Real 33765 | Hollerith 3862 | Integer 52240 | Max Pairs 1 | nblistReal 0 | nblist Int 0 ! | Total 482 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN --- 54,70 ---- IFBOX = 0 NMXRS = 35 IFCAP = 0 NEXTRA = 0 NCOPY = 0 | Memory Use Allocated ! | Real 35725 | Hollerith 3862 | Integer 52240 | Max Pairs 1 | nblistReal 0 | nblist Int 0 ! | Total 498 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN *************** *** 138,155 **** Here are comments from the DISANG input file: ****** C4' ( 134)-C4' ( 485) NSTEP1= 0 NSTEP2= 1000 R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000 ! R1A= -85.000 R2A= 20.000 R3A= 20.000 R4A= 115.000 RK2A=5000.000 RK3A= 5000.000 Rcurr: 15.124 Rcurr-(R2+R3)/2: 0.124 MIN(Rcurr-R2,Rcurr-R3): 0.124 Number of restraints read = 1 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 0 -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- --- 138,159 ---- Here are comments from the DISANG input file: ****** C4' ( 134)-C4' ( 485) NSTEP1= 0 NSTEP2= 1000 R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000 ! R1A= -80.000 R2A= 20.000 R3A= 20.000 R4A= 120.000 RK2A=5000.000 RK3A= 5000.000 Rcurr: 15.124 Rcurr-(R2+R3)/2: 0.124 MIN(Rcurr-R2,Rcurr-R3): 0.124 Number of restraints read = 1 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 0 + | Atom division among processors: + | 0 320 640 + | Running AMBER/MPI version on 2 nodes + -------------------------------------------------------------------------------- 4. RESULTS -------------------------------------------------------------------------------- *************** *** 304,339 **** ------------------------------------------------------------------------------ First atom Last atom curr. value target deviation penalty ------------------------------------------------------------------------------ C4' RC 5 -- C4' RG 16: 20.017 20.000 0.017 1.417 d 0: 0 Total distance penalty: 1.417 - | RMS deviation from ideal bonds : 0.0280 - | RMS deviation from ideal angles: 4.219 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.04% of Total) ! | Calc gb radii 17.68 (30.09% of Gen B) ! | Calc gb diag 30.54 (51.96% of Gen B) ! | Calc gb off-diag 10.54 (17.94% of Gen B) ! | Other 0.00 ( 0.01% of Gen B) ! | Gen Born time 58.76 (100.0% of Nonbo) ! | Nonbond force 58.76 (97.64% of Force) ! | Bond/Angle/Dihedral 1.37 ( 2.27% of Force) ! | Other 0.05 ( 0.08% of Force) ! | Force time 60.18 (99.08% of Runmd) ! | Shake time 0.05 ( 0.08% of Runmd) ! | Verlet update time 0.50 ( 0.83% of Runmd) | Other 0.01 ( 0.01% of Runmd) ! | Runmd Time 60.74 (99.82% of Total) ! | Other 0.09 ( 0.15% of Total) ! | Total time 60.85 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 17:33:44.650 on 02/13/2007 ! | Setup done at 17:33:44.766 on 02/13/2007 ! | Run done at 17:34:45.509 on 02/13/2007 ! | wallclock() was called 24010 times --- 308,346 ---- ------------------------------------------------------------------------------ First atom Last atom curr. value target deviation penalty ------------------------------------------------------------------------------ C4' RC 5 -- C4' RG 16: 20.017 20.000 0.017 1.417 d 0: 0 Total distance penalty: 1.417 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- ! |>>>>>>>>PROFILE of Average TIMES>>>>>>>>> ! | Calc gb radii 12.38 (20.57% of Gen B) ! | Communicate gb radii 13.48 (22.39% of Gen B) ! | Calc gb diag 24.84 (41.25% of Gen B) ! | Calc gb off-diag 9.51 (15.78% of Gen B) ! | Other 0.01 ( 0.01% of Gen B) ! | Gen Born time 60.22 (100.0% of Nonbo) ! | Nonbond force 60.22 (87.08% of Force) ! | Bond/Angle/Dihedral 0.77 ( 1.12% of Force) ! | FRC Collect time 1.29 ( 1.86% of Force) ! | Other 6.88 ( 9.94% of Force) ! | Force time 69.16 (92.42% of Runmd) ! | Shake time 0.04 ( 0.05% of Runmd) ! | Verlet update time 2.90 ( 3.87% of Runmd) ! | CRD distribute time 2.73 ( 3.65% of Runmd) | Other 0.01 ( 0.01% of Runmd) ! | Runmd Time 74.83 (99.89% of Total) ! | Other 0.08 ( 0.11% of Total) ! | Total time 74.92 (100.0% of ALL ) ! ! | Number of list builds : 0 | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 16:57:21.497 on 08/29/2007 ! | Setup done at 16:57:21.562 on 08/29/2007 ! | Run done at 16:58:36.424 on 08/29/2007 ! | wallclock() was called 35010 times *** test/jar_multi/mdout.jar.000.save_old 2007-08-29 15:28:51.000000000 -0400 --- test/jar_multi/mdout.jar.000.save 2007-08-29 17:00:09.000000000 -0400 *************** *** 1,11 **** ------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 02/13/2007 at 18:14:06 [-O]verwriting output File Assignments: | MDIN: gbin.000 | MDOUT: mdout.jar.000 --- 1,11 ---- ------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 08/29/2007 at 16:58:40 [-O]verwriting output File Assignments: | MDIN: gbin.000 | MDOUT: mdout.jar.000 *************** *** 138,148 **** Here are comments from the DISANG input file: ****** C4' ( 134)-C4' ( 485) NSTEP1= 0 NSTEP2= 1000 R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000 ! R1A= -85.000 R2A= 20.000 R3A= 20.000 R4A= 115.000 RK2A=5000.000 RK3A= 5000.000 Rcurr: 15.124 Rcurr-(R2+R3)/2: 0.124 MIN(Rcurr-R2,Rcurr-R3): 0.124 Number of restraints read = 1 Done reading weight changes/NMR restraints --- 138,148 ---- Here are comments from the DISANG input file: ****** C4' ( 134)-C4' ( 485) NSTEP1= 0 NSTEP2= 1000 R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000 ! R1A= -80.000 R2A= 20.000 R3A= 20.000 R4A= 120.000 RK2A=5000.000 RK3A= 5000.000 Rcurr: 15.124 Rcurr-(R2+R3)/2: 0.124 MIN(Rcurr-R2,Rcurr-R3): 0.124 Number of restraints read = 1 Done reading weight changes/NMR restraints *************** *** 315,342 **** -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.03% of Total) ! | Calc gb radii 17.69 (30.58% of Gen B) ! | Calc gb diag 29.95 (51.77% of Gen B) ! | Calc gb off-diag 10.20 (17.63% of Gen B) ! | Other 0.01 ( 0.01% of Gen B) ! | Gen Born time 57.84 (100.0% of Nonbo) ! | Nonbond force 57.84 (97.61% of Force) ! | Bond/Angle/Dihedral 1.37 ( 2.31% of Force) ! | Other 0.05 ( 0.08% of Force) ! | Force time 59.26 (99.09% of Runmd) ! | Shake time 0.05 ( 0.09% of Runmd) ! | Verlet update time 0.49 ( 0.81% of Runmd) | Other 0.01 ( 0.01% of Runmd) ! | Runmd Time 59.81 (99.84% of Total) ! | Other 0.07 ( 0.12% of Total) ! | Total time 59.90 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 18:14:06.679 on 02/13/2007 ! | Setup done at 18:14:06.774 on 02/13/2007 ! | Run done at 18:15:06.581 on 02/13/2007 | wallclock() was called 33010 times --- 315,342 ---- -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.01 ( 0.01% of Total) ! | Calc gb radii 23.56 (27.15% of Gen B) ! | Calc gb diag 45.86 (52.85% of Gen B) ! | Calc gb off-diag 17.34 (19.99% of Gen B) ! | Other 0.00 ( 0.01% of Gen B) ! | Gen Born time 86.77 (100.0% of Nonbo) ! | Nonbond force 86.77 (98.29% of Force) ! | Bond/Angle/Dihedral 1.45 ( 1.64% of Force) ! | Other 0.06 ( 0.07% of Force) ! | Force time 88.29 (99.36% of Runmd) ! | Shake time 0.05 ( 0.06% of Runmd) ! | Verlet update time 0.50 ( 0.57% of Runmd) | Other 0.01 ( 0.01% of Runmd) ! | Runmd Time 88.85 (100.0% of Total) ! | Other 0.03 ( 0.03% of Total) ! | Total time 88.89 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 16:58:40.784 on 08/29/2007 ! | Setup done at 16:58:40.815 on 08/29/2007 ! | Run done at 17:00:09.670 on 08/29/2007 | wallclock() was called 33010 times *** test/jar_multi/mdout.jar.001.save_old 2007-08-29 15:28:51.000000000 -0400 --- test/jar_multi/mdout.jar.001.save 2007-08-29 17:00:09.000000000 -0400 *************** *** 1,11 **** ------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 02/13/2007 at 18:14:06 [-O]verwriting output File Assignments: | MDIN: gbin.001 | MDOUT: mdout.jar.001 --- 1,11 ---- ------------------------------------------------------- Amber 9 SANDER 2006 ------------------------------------------------------- ! | Run on 08/29/2007 at 16:58:40 [-O]verwriting output File Assignments: | MDIN: gbin.001 | MDOUT: mdout.jar.001 *************** *** 138,148 **** Here are comments from the DISANG input file: ****** C4' ( 134)-C4' ( 485) NSTEP1= 0 NSTEP2= 1000 R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000 ! R1A= -85.000 R2A= 20.000 R3A= 20.000 R4A= 115.000 RK2A=5000.000 RK3A= 5000.000 Rcurr: 15.124 Rcurr-(R2+R3)/2: 0.124 MIN(Rcurr-R2,Rcurr-R3): 0.124 Number of restraints read = 1 Done reading weight changes/NMR restraints --- 138,148 ---- Here are comments from the DISANG input file: ****** C4' ( 134)-C4' ( 485) NSTEP1= 0 NSTEP2= 1000 R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000 ! R1A= -80.000 R2A= 20.000 R3A= 20.000 R4A= 120.000 RK2A=5000.000 RK3A= 5000.000 Rcurr: 15.124 Rcurr-(R2+R3)/2: 0.124 MIN(Rcurr-R2,Rcurr-R3): 0.124 Number of restraints read = 1 Done reading weight changes/NMR restraints *************** *** 258,271 **** NMR restraints: Bond = 0.004 Angle = 0.000 Torsion = 0.000 =============================================================================== | RE_POSITION Moving by -0.111645 -0.200871 -0.094889 NSTEP = 1000 TIME(PS) = 132.000 TEMP(K) = 283.15 PRESS = 0.0 ! Etot = -3538.3784 EKtot = 478.2764 EPtot = -4016.6548 BOND = 195.3637 ANGLE = 337.5911 DIHED = 431.5481 1-4 NB = 169.2287 1-4 EEL = -2305.1135 VDWAALS = -326.8382 ! EELEC = -18.4199 EGB = -2503.6434 RESTRAINT = 3.6286 EAMBER (non-restraint) = -4020.2834 ------------------------------------------------------------------------------ NMR restraints: Bond = 3.629 Angle = 0.000 Torsion = 0.000 =============================================================================== --- 258,271 ---- NMR restraints: Bond = 0.004 Angle = 0.000 Torsion = 0.000 =============================================================================== | RE_POSITION Moving by -0.111645 -0.200871 -0.094889 NSTEP = 1000 TIME(PS) = 132.000 TEMP(K) = 283.15 PRESS = 0.0 ! Etot = -3538.3785 EKtot = 478.2764 EPtot = -4016.6548 BOND = 195.3637 ANGLE = 337.5911 DIHED = 431.5481 1-4 NB = 169.2287 1-4 EEL = -2305.1135 VDWAALS = -326.8382 ! EELEC = -18.4200 EGB = -2503.6434 RESTRAINT = 3.6286 EAMBER (non-restraint) = -4020.2834 ------------------------------------------------------------------------------ NMR restraints: Bond = 3.629 Angle = 0.000 Torsion = 0.000 =============================================================================== *************** *** 315,342 **** -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.02 ( 0.03% of Total) ! | Calc gb radii 17.54 (30.18% of Gen B) ! | Calc gb diag 30.07 (51.73% of Gen B) ! | Calc gb off-diag 10.51 (18.08% of Gen B) | Other 0.00 ( 0.01% of Gen B) ! | Gen Born time 58.12 (100.0% of Nonbo) ! | Nonbond force 58.13 (97.61% of Force) ! | Bond/Angle/Dihedral 1.37 ( 2.30% of Force) ! | Other 0.05 ( 0.08% of Force) ! | Force time 59.55 (99.10% of Runmd) ! | Shake time 0.05 ( 0.09% of Runmd) ! | Verlet update time 0.48 ( 0.80% of Runmd) | Other 0.01 ( 0.01% of Runmd) ! | Runmd Time 60.09 (99.85% of Total) ! | Other 0.08 ( 0.13% of Total) ! | Total time 60.18 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 18:14:06.679 on 02/13/2007 ! | Setup done at 18:14:06.774 on 02/13/2007 ! | Run done at 18:15:06.863 on 02/13/2007 | wallclock() was called 33010 times --- 315,342 ---- -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- ! | Read coords time 0.01 ( 0.01% of Total) ! | Calc gb radii 23.64 (27.22% of Gen B) ! | Calc gb diag 45.47 (52.36% of Gen B) ! | Calc gb off-diag 17.72 (20.41% of Gen B) | Other 0.00 ( 0.01% of Gen B) ! | Gen Born time 86.83 (100.0% of Nonbo) ! | Nonbond force 86.83 (98.14% of Force) ! | Bond/Angle/Dihedral 1.55 ( 1.75% of Force) ! | Other 0.10 ( 0.11% of Force) ! | Force time 88.48 (99.37% of Runmd) ! | Shake time 0.05 ( 0.06% of Runmd) ! | Verlet update time 0.50 ( 0.56% of Runmd) | Other 0.01 ( 0.01% of Runmd) ! | Runmd Time 89.04 (100.0% of Total) ! | Other 0.03 ( 0.03% of Total) ! | Total time 89.07 (100.0% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 ! | Job began at 16:58:40.784 on 08/29/2007 ! | Setup done at 16:58:40.815 on 08/29/2007 ! | Run done at 17:00:09.855 on 08/29/2007 | wallclock() was called 33010 times ------------------------------------------------------------------------------ Temporary workarounds: none