********>Bugfix 28: Author: Matthew Seetin Date: 10/15/2009 Programs: sander Description: This patch contains a few updates to NMR restraints in sander and pmemd. 1. Sander: Fix a bug in which torsion restraints involving at least one center of mass group would not operate on the correct atoms 2. Sander: Fix a bug in which any restraint involving at least one center of mass group AND at least one single atom would not apply the y and z components of the force correctly 3. Sander: Fix a bug in plane-plane and plane-point restraints where if the vectors defining the plane(s) were parallel, the force would blow up due to a division by 0 (or a really small #). 4. Sander: Fix a bug affecting all COM distance restraints where the force applied to the atoms that make up the COM group is mistakenly applied twice. 5. pmemd: Fix the same behavior as bug #2 that was also present in pmemd. 6. Test cases: test cases updated to give correct output in light of the bug fixes. Fix: apply the following patch to amber10/src/sander/nmr.f, amber10/src/pmemd/src/nmr_lib.fpp, and the test cases in test/plane_plane_restraint Usage: Save this file in your $AMBERHOME directory and then apply this patch file to your amber 10 distribution as follows: cd $AMBERHOME patch -p0 -N -r patch_rejects 3) and position two (elements 4->6). - ! NMRAT(4,I) + ! DFR(24): d(E)/d(x_com),d(E)/d(y_com) and d(E)/d(z_com) for position one + ! (elements 1->3), position two (elements 4->6), etc. + ! NMRAT(16,I) ! NMRCOM(2,I): Define the group of atoms used to calculate the center of mass. ! If NMRAT(1,I) < 0, then ! (NMRCOM(1,K) -> NMRCOM(2,K)), K=-NMRAT(1,I),-NMRAT(3,I) @@ -2961,8 +2970,8 @@ ! If NMRAT(2,I) < 0, then ! (NMRCOM(1,K) -> NMRCOM(2,K)), K=-NMRAT(2,I),-NMRAT(4,I) ! gives the atoms in the group whose center of mass is position 2. - ! RMSTOT(2): The total masses for all the atoms defining the group at each - ! end of the distance restraint. + ! RMSTOT(8): The total masses for all the atoms defining the group for each + ! atom or COM group of the restraint. ! RIMASS(I): The inverse mass for atom I. ! I: The number of the restraint in the list. @@ -2971,7 +2980,7 @@ dimension f(*),dfr(*),nmrat(16,*),nmrcom(2,*),rimass(*) dimension rmstot(8) - ! Loop over both ends of the distance restraint: + ! Loop over all atoms or COM groups in the restraint: do 5 iat = 1,8 jatm = 3*(iat-1) @@ -2980,6 +2989,10 @@ ! by the derivatives in DF, and add them into the force array. if (nmrat(iat,i) < 0 .and. nmrat(iat+8,i) < 0) then + + ! See the comments in the NMRGRP subroutine for more information about + ! the non-intuitive scheme for looping over all atoms in a COM below. + do 10 ip = -nmrat(iat,i),-nmrat(8+iat,i) do 20 j = nmrcom(1,ip),nmrcom(2,ip) jx = 3*(j-1) @@ -2990,13 +3003,13 @@ f(jx+3) = f(jx+3) - dfr(jatm+3)*dcomdx 20 continue 10 continue - else if (nmrat(iat,i) > 0) then + else if (nmrat(iat,i) >= 0) then ! Standard derivatives if no group defined: jx = nmrat(iat,i) do 30 m = 1,3 - f(jx+m) = f(jx+m) - dfr(jatm+1) + f(jx+m) = f(jx+m) - dfr(jatm+m) 30 continue end if 5 continue @@ -3025,6 +3038,8 @@ dimension x(*),xcom(24),nmrat(16,*),nmrcom(2,*),rimass(*),ricmmass(8) dimension rmstot(8) + ! Loop over all atoms or COMs that make up the restraint + do 5 iat = 1,8 xtot = 0.0d0 ytot = 0.0d0 @@ -3034,6 +3049,10 @@ ifill = 3*(iat-1) if (nmrat(iat,i) < 0) then + + ! See the comments in the NMRGRP subroutine for more information about + ! the non-intuitive scheme for looping over all atoms in a COM below. + do 10 ip = -nmrat(iat,i),-nmrat(8+iat,i) do 20 j = nmrcom(1,ip),nmrcom(2,ip) @@ -3089,7 +3108,7 @@ ! (NMRCOM(1,K) -> NMRCOM(2,K)), K=-NMRAT(2,I), -NMRAT(10,I) - ! and so on up through NMRAT(8,I) and NMR(16,I) if that many groups are defined + ! and so on up through NMRAT(8,I) and NMRAT(16,I) if that many groups are defined ! If IRESID = 1: IGR(I) is the residue # for atom I, and GRNAM(I) is the ! corresponding atom name. @@ -3490,7 +3509,7 @@ nave(1),nexact(1),ipower(1),tauave(1), & ravein(1),dt,navint(1),iave,incflg(1), & ifirst,2,ialtdis(i)) - call nmrcmf(f,dfr,nmrat,nmrcom,rmstot,rimass,i) +! There was a bug here with an extra instance of a call to nmrcmf if(ifconstr(i) > 0) call vec_constr(xcom,f,dfr,ricmmass,dt,rint, & 0,3,tgtvec(3*(i-1)+1),1) call nmrcmf(f,dfr,nmrat,nmrcom,rmstot,rimass,i) @@ -3524,7 +3543,7 @@ if (.not.jcoupl) then if (usecom) then call nmrcms(x,xcom,nmrat,nmrcom,rmstot,rimass,ricmmass,i) - call tornrg(x,f,dfr,rint,0,3,6,9, & + call tornrg(xcom,f,dfr,rint,0,3,6,9, & e,r1,r2,r3,r4,rk2,rk3,ntb, & tave1(2*i-1),tave01(i),tave2(2*i-1), & tave02(i),nave(3),nexact(3),ipower(3), & @@ -7278,11 +7297,19 @@ n2(2) = -xef(1)*xgh(3) + xef(3)*xgh(1) n2(3) = xef(1)*xgh(2) - xef(2)*xgh(1) - ! Calculate angle from n1*n2 = cos(theta) - rdenom1 = sqrt(n1(1)**2 + n1(2)**2 + n1(3)**2) rdenom2 = sqrt(n2(1)**2 + n2(2)**2 + n2(3)**2) + ! If the vectors defining either plane are parallel, we cannot calculate a value for + ! this restraint, so set energy to zero and return: + + if (rdenom1 < 0.1d0 .or. rdenom2 < 0.1d0) then + e = 0.0d0 + return + end if + + ! Calculate angle from n1*n2 = cos(theta) + cst = (n1(1)*n2(1) + n1(2)*n2(2) + n1(3)*n2(3))/rdenom1/rdenom2 if (cst > 1.0d0) cst = 1.0d0 if (cst < -1.0d0) cst = -1.0d0 @@ -7579,10 +7606,17 @@ n1(2) = -xab(1)*xcd(3) + xab(3)*xcd(1) n1(3) = xab(1)*xcd(2) - xab(2)*xcd(1) - - ! Calculate angle from n1*(x(i5)-plncom) = cos(theta) - rdenom1 = sqrt(n1(1)**2 + n1(2)**2 + n1(3)**2) + + ! If the vectors defining the plane are parallel, we cannot calculate a value for + ! this restraint, so set energy to zero and return: + + if (rdenom1 < 0.001d0) then + e = 0.0d0 + return + end if + + ! Calculate angle from n1*(x(i5)-plncom) = cos(theta) cst = (n1(1)*vector2(1) + n1(2)*vector2(2) + n1(3)*vector2(3))/rdenom1/rdenom2 --- test/plane_plane_restraint/dinuc_pln_vs_t.save 2007-11-20 18:25:26.000000000 -0500 +++ test/plane_plane_restraint/dinuc_pln_vs_t.save 2009-10-14 17:53:22.000000000 -0400 @@ -1,10 +1,10 @@ 0 165.762 6.532 1 165.746 6.532 2 165.751 6.532 - 3 165.774 6.531 - 4 165.814 6.530 - 5 165.871 6.528 - 6 165.942 6.526 - 7 166.025 6.524 - 8 166.117 6.521 - 9 166.219 6.518 + 3 165.774 6.532 + 4 165.815 6.531 + 5 165.871 6.530 + 6 165.942 6.528 + 7 166.025 6.527 + 8 166.118 6.525 + 9 166.219 6.523 --- test/plane_plane_restraint/dinuc_plpt_vs_t.save 2008-01-23 13:27:41.000000000 -0500 +++ test/plane_plane_restraint/dinuc_plpt_vs_t.save 2009-10-14 17:53:31.000000000 -0400 @@ -1,10 +1,10 @@ 0 90.047 6.532 - 1 90.011 6.532 - 2 89.974 6.532 - 3 89.938 6.531 - 4 89.902 6.530 - 5 89.867 6.528 - 6 89.833 6.526 - 7 89.799 6.524 - 8 89.767 6.521 - 9 89.735 6.518 + 1 90.035 6.532 + 2 90.045 6.532 + 3 90.079 6.532 + 4 90.137 6.531 + 5 90.216 6.530 + 6 90.317 6.528 + 7 90.438 6.527 + 8 90.578 6.525 + 9 90.735 6.523 --- test/plane_plane_restraint/mdout.dinucAU_plpt.save 2008-03-17 22:15:08.000000000 -0400 +++ test/plane_plane_restraint/mdout.dinucAU_plpt.save 2009-10-14 17:54:19.000000000 -0400 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 02/06/2008 at 17:03:35 +| Run on 10/14/2009 at 16:13:58 [-O]verwriting output File Assignments: @@ -17,9 +17,12 @@ | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo +| MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip +|INPTRA: inptraj +| Here is the input file: @@ -58,12 +61,12 @@ | Memory Use Allocated | Real 3524 -| Hollerith 370 +| Hollerith 187 | Integer 23437 | Max Pairs 1 | nblistReal 0 | nblist Int 0 -| Total 120 kbytes +| Total 119 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals @@ -170,8 +173,8 @@ | NDFMIN = 152. NUM_NOSHAKE = 0 CORRECTED RNDFP = 152. | TOTAL # of degrees of freedom (RNDF) = 152. - NSTEP = 1 TIME(PS) = 0.011 TEMP(K) = 204.49 PRESS = 0.0 - Etot = 43.6304 EKtot = 30.8842 EPtot = 12.7463 + NSTEP = 1 TIME(PS) = 0.011 TEMP(K) = 204.28 PRESS = 0.0 + Etot = 43.5973 EKtot = 30.8510 EPtot = 12.7463 BOND = 5.5498 ANGLE = 43.4372 DIHED = 37.8640 1-4 NB = 18.2261 1-4 EEL = -9.8751 VDWAALS = -2.1293 EELEC = -96.1686 EGB = -65.1442 RESTRAINT = 80.9865 @@ -182,138 +185,138 @@ : Plane-Point = 73.944 Plane-Plane = 0.000 =============================================================================== - NSTEP = 2 TIME(PS) = 0.012 TEMP(K) = 145.78 PRESS = 0.0 - Etot = 43.8671 EKtot = 22.0159 EPtot = 21.8512 - BOND = 5.2054 ANGLE = 51.9114 DIHED = 38.0227 - 1-4 NB = 18.6519 1-4 EEL = -10.3124 VDWAALS = -1.2592 - EELEC = -96.1928 EGB = -65.2237 RESTRAINT = 81.0479 - EAMBER (non-restraint) = -59.1967 + NSTEP = 2 TIME(PS) = 0.012 TEMP(K) = 145.31 PRESS = 0.0 + Etot = 43.7541 EKtot = 21.9459 EPtot = 21.8082 + BOND = 5.2036 ANGLE = 51.9126 DIHED = 38.0183 + 1-4 NB = 18.6504 1-4 EEL = -10.3119 VDWAALS = -1.2598 + EELEC = -96.1914 EGB = -65.2232 RESTRAINT = 81.0097 + EAMBER (non-restraint) = -59.2015 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.043 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.004 Plane-Plane = 0.000 + NMR restraints: Bond = 7.044 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.965 Plane-Plane = 0.000 =============================================================================== - NSTEP = 3 TIME(PS) = 0.013 TEMP(K) = 125.53 PRESS = 0.0 - Etot = 43.9853 EKtot = 18.9580 EPtot = 25.0273 - BOND = 4.7888 ANGLE = 55.2275 DIHED = 38.1410 - 1-4 NB = 18.7486 1-4 EEL = -10.6758 VDWAALS = -0.8017 - EELEC = -96.1690 EGB = -65.3376 RESTRAINT = 81.1054 - EAMBER (non-restraint) = -56.0781 + NSTEP = 3 TIME(PS) = 0.013 TEMP(K) = 125.08 PRESS = 0.0 + Etot = 43.7890 EKtot = 18.8898 EPtot = 24.8992 + BOND = 4.7841 ANGLE = 55.2310 DIHED = 38.1285 + 1-4 NB = 18.7433 1-4 EEL = -10.6744 VDWAALS = -0.8038 + EELEC = -96.1650 EGB = -65.3359 RESTRAINT = 80.9913 + EAMBER (non-restraint) = -56.0921 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.041 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.065 Plane-Plane = 0.000 + NMR restraints: Bond = 7.044 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.948 Plane-Plane = 0.000 =============================================================================== - NSTEP = 4 TIME(PS) = 0.014 TEMP(K) = 147.44 PRESS = 0.0 - Etot = 43.9847 EKtot = 22.2679 EPtot = 21.7168 - BOND = 4.7093 ANGLE = 52.6324 DIHED = 38.2085 - 1-4 NB = 18.4200 1-4 EEL = -10.9812 VDWAALS = -0.8659 - EELEC = -96.0796 EGB = -65.4851 RESTRAINT = 81.1583 - EAMBER (non-restraint) = -59.4415 + NSTEP = 4 TIME(PS) = 0.014 TEMP(K) = 147.24 PRESS = 0.0 + Etot = 43.7020 EKtot = 22.2375 EPtot = 21.4646 + BOND = 4.7012 ANGLE = 52.6400 DIHED = 38.1859 + 1-4 NB = 18.4086 1-4 EEL = -10.9787 VDWAALS = -0.8702 + EELEC = -96.0719 EGB = -65.4816 RESTRAINT = 80.9312 + EAMBER (non-restraint) = -59.4666 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.034 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.124 Plane-Plane = 0.000 + NMR restraints: Bond = 7.040 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.891 Plane-Plane = 0.000 =============================================================================== - NSTEP = 5 TIME(PS) = 0.015 TEMP(K) = 202.58 PRESS = 0.0 - Etot = 43.8871 EKtot = 30.5952 EPtot = 13.2918 - BOND = 5.3803 ANGLE = 45.0380 DIHED = 38.2371 - 1-4 NB = 17.7432 1-4 EEL = -11.2598 VDWAALS = -1.4911 - EELEC = -95.8973 EGB = -65.6647 RESTRAINT = 81.2061 - EAMBER (non-restraint) = -67.9143 + NSTEP = 5 TIME(PS) = 0.015 TEMP(K) = 202.84 PRESS = 0.0 + Etot = 43.5154 EKtot = 30.6340 EPtot = 12.8814 + BOND = 5.3680 ANGLE = 45.0526 DIHED = 38.2049 + 1-4 NB = 17.7238 1-4 EEL = -11.2561 VDWAALS = -1.4982 + EELEC = -95.8846 EGB = -65.6590 RESTRAINT = 80.8300 + EAMBER (non-restraint) = -67.9486 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.023 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.183 Plane-Plane = 0.000 + NMR restraints: Bond = 7.033 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.797 Plane-Plane = 0.000 =============================================================================== - NSTEP = 6 TIME(PS) = 0.016 TEMP(K) = 272.23 PRESS = 0.0 - Etot = 43.7443 EKtot = 41.1145 EPtot = 2.6298 - BOND = 7.0761 ANGLE = 34.7294 DIHED = 38.2556 - 1-4 NB = 16.9045 1-4 EEL = -11.5511 VDWAALS = -2.5729 - EELEC = -95.5932 EGB = -65.8674 RESTRAINT = 81.2487 - EAMBER (non-restraint) = -78.6189 + NSTEP = 6 TIME(PS) = 0.016 TEMP(K) = 273.13 PRESS = 0.0 + Etot = 43.2812 EKtot = 41.2493 EPtot = 2.0319 + BOND = 7.0577 ANGLE = 34.7549 DIHED = 38.2175 + 1-4 NB = 16.8759 1-4 EEL = -11.5462 VDWAALS = -2.5837 + EELEC = -95.5742 EGB = -65.8590 RESTRAINT = 80.6890 + EAMBER (non-restraint) = -78.6570 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.008 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.241 Plane-Plane = 0.000 + NMR restraints: Bond = 7.022 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.667 Plane-Plane = 0.000 =============================================================================== - NSTEP = 7 TIME(PS) = 0.017 TEMP(K) = 333.97 PRESS = 0.0 - Etot = 43.6408 EKtot = 50.4387 EPtot = -6.7979 - BOND = 9.8004 ANGLE = 24.6888 DIHED = 38.2989 - 1-4 NB = 16.0816 1-4 EEL = -11.8946 VDWAALS = -3.8371 - EELEC = -95.1493 EGB = -66.0729 RESTRAINT = 81.2863 - EAMBER (non-restraint) = -88.0842 + NSTEP = 7 TIME(PS) = 0.017 TEMP(K) = 335.66 PRESS = 0.0 + Etot = 43.0838 EKtot = 50.6929 EPtot = -7.6091 + BOND = 9.7721 ANGLE = 24.7283 DIHED = 38.2622 + 1-4 NB = 16.0437 1-4 EEL = -11.8888 VDWAALS = -3.8522 + EELEC = -95.1227 EGB = -66.0617 RESTRAINT = 80.5099 + EAMBER (non-restraint) = -88.1191 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.989 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.297 Plane-Plane = 0.000 + NMR restraints: Bond = 7.008 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.502 Plane-Plane = 0.000 =============================================================================== - NSTEP = 8 TIME(PS) = 0.018 TEMP(K) = 369.54 PRESS = 0.0 - Etot = 43.6533 EKtot = 55.8107 EPtot = -12.1574 - BOND = 13.2100 ANGLE = 17.6626 DIHED = 38.3913 - 1-4 NB = 15.3757 1-4 EEL = -12.3226 VDWAALS = -4.9700 - EELEC = -94.5687 EGB = -66.2551 RESTRAINT = 81.3194 - EAMBER (non-restraint) = -93.4769 + NSTEP = 8 TIME(PS) = 0.018 TEMP(K) = 372.16 PRESS = 0.0 + Etot = 42.9998 EKtot = 56.2057 EPtot = -13.2059 + BOND = 13.1670 ANGLE = 17.7177 DIHED = 38.3665 + 1-4 NB = 15.3285 1-4 EEL = -12.3163 VDWAALS = -4.9904 + EELEC = -94.5330 EGB = -66.2413 RESTRAINT = 80.2955 + EAMBER (non-restraint) = -93.5013 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.967 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.352 Plane-Plane = 0.000 + NMR restraints: Bond = 6.992 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.303 Plane-Plane = 0.000 =============================================================================== - NSTEP = 9 TIME(PS) = 0.019 TEMP(K) = 371.13 PRESS = 0.0 - Etot = 43.7999 EKtot = 56.0505 EPtot = -12.2506 - BOND = 16.6499 ANGLE = 15.3186 DIHED = 38.5331 - 1-4 NB = 14.8128 1-4 EEL = -12.8546 VDWAALS = -5.7951 - EELEC = -93.8766 EGB = -66.3876 RESTRAINT = 81.3488 - EAMBER (non-restraint) = -93.5994 + NSTEP = 9 TIME(PS) = 0.019 TEMP(K) = 374.81 PRESS = 0.0 + Etot = 43.0478 EKtot = 56.6065 EPtot = -13.5587 + BOND = 16.5870 ANGLE = 15.3878 DIHED = 38.5336 + 1-4 NB = 14.7565 1-4 EEL = -12.8484 VDWAALS = -5.8221 + EELEC = -93.8299 EGB = -66.3716 RESTRAINT = 80.0484 + EAMBER (non-restraint) = -93.6071 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.943 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.406 Plane-Plane = 0.000 + NMR restraints: Bond = 6.974 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 73.074 Plane-Plane = 0.000 =============================================================================== - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 342.88 PRESS = 0.0 - Etot = 44.0458 EKtot = 51.7847 EPtot = -7.7389 - BOND = 19.3239 ANGLE = 17.8424 DIHED = 38.7032 - 1-4 NB = 14.3769 1-4 EEL = -13.4970 VDWAALS = -6.3085 - EELEC = -93.1128 EGB = -66.4423 RESTRAINT = 81.3753 - EAMBER (non-restraint) = -89.1142 + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 347.75 PRESS = 0.0 + Etot = 43.1928 EKtot = 52.5194 EPtot = -9.3266 + BOND = 19.2374 ANGLE = 17.9216 DIHED = 38.7446 + 1-4 NB = 14.3112 1-4 EEL = -13.4915 VDWAALS = -6.3438 + EELEC = -93.0533 EGB = -66.4249 RESTRAINT = 79.7720 + EAMBER (non-restraint) = -89.0987 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.917 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.459 Plane-Plane = 0.000 + NMR restraints: Bond = 6.954 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 72.818 Plane-Plane = 0.000 =============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 251.56 PRESS = 0.0 - Etot = 43.8239 EKtot = 37.9920 EPtot = 5.8318 - BOND = 9.1694 ANGLE = 35.8488 DIHED = 38.2655 - 1-4 NB = 16.9341 1-4 EEL = -11.5224 VDWAALS = -3.0031 - EELEC = -95.2808 EGB = -65.7881 RESTRAINT = 81.2083 - EAMBER (non-restraint) = -75.3764 + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 252.82 PRESS = 0.0 + Etot = 43.3963 EKtot = 38.1832 EPtot = 5.2131 + BOND = 9.1428 ANGLE = 35.8784 DIHED = 38.2526 + 1-4 NB = 16.9068 1-4 EEL = -11.5188 VDWAALS = -3.0153 + EELEC = -95.2595 EGB = -65.7802 RESTRAINT = 80.6064 + EAMBER (non-restraint) = -75.3932 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.917 Angle = 0.000 Torsion = 0.000 - : Plane-Point = 74.459 Plane-Plane = 0.000 + NMR restraints: Bond = 6.954 Angle = 0.000 Torsion = 0.000 + : Plane-Point = 72.818 Plane-Plane = 0.000 =============================================================================== R M S F L U C T U A T I O N S - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 92.90 PRESS = 0.0 - Etot = 0.1463 EKtot = 14.0304 EPtot = 14.0904 - BOND = 5.1228 ANGLE = 15.0317 DIHED = 0.2280 - 1-4 NB = 1.5802 1-4 EEL = 1.0821 VDWAALS = 1.9742 - EELEC = 1.0354 EGB = 0.4622 RESTRAINT = 0.1248 - EAMBER (non-restraint) = 13.9656 + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 94.49 PRESS = 0.0 + Etot = 0.2935 EKtot = 14.2708 EPtot = 14.5608 + BOND = 5.0956 ANGLE = 15.0053 DIHED = 0.2373 + 1-4 NB = 1.6023 1-4 EEL = 1.0800 VDWAALS = 1.9851 + EELEC = 1.0546 EGB = 0.4560 RESTRAINT = 0.4161 + EAMBER (non-restraint) = 14.1448 ------------------------------------------------------------------------------ @@ -330,40 +333,39 @@ ------------------------------------------------------------------------------ First atom Last atom curr. value target deviation penalty ------------------------------------------------------------------------------ - N9 RAN 1 -- *C2 RUN 2: 89.704 180.000 90.296 74.510 p - *N3 RAN 1 -- *C2 RUN 2: 6.515 5.000 1.515 6.890 d 0: 0 - Total distance penalty: 6.890 - Total plane-point angle penalty: 74.510 -| RMS deviation from ideal bonds : 0.0384 -| RMS deviation from ideal angles: 3.306 + N9 RAN 1 -- *C2 RUN 2: 90.909 180.000 89.091 72.535 p + *N3 RAN 1 -- *C2 RUN 2: 6.520 5.000 1.520 6.935 d 0: 0 + Total distance penalty: 6.935 + Total plane-point angle penalty: 72.535 +| RMS deviation from ideal bonds : 0.0383 +| RMS deviation from ideal angles: 3.314 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.00 ( 2.16% of Total) -| Fast Water setup 0.00 ( 0.08% of Total) -| Calc gb radii 0.00 (26.03% of Gen B) -| Calc gb diag 0.00 (36.09% of Gen B) -| Calc gb off-diag 0.00 (37.15% of Gen B) -| Other 0.00 ( 0.73% of Gen B) -| Gen Born time 0.01 (99.84% of Nonbo) -| IPS excludes 0.00 ( 0.16% of Nonbo) -| Nonbond force 0.01 (81.81% of Force) -| Bond/Angle/Dihedral 0.00 (13.69% of Force) -| Other 0.00 ( 4.50% of Force) -| Force time 0.01 (72.50% of Runmd) -| Shake time 0.00 ( 0.59% of Runmd) -| Verlet update time 0.00 (20.88% of Runmd) -| Other 0.00 ( 6.03% of Runmd) -| Runmd Time 0.01 (68.80% of Total) -| Other 0.00 (28.95% of Total) -| Total time 0.02 (99.55% of ALL ) +| Read coords time 0.00 ( 1.50% of Total) +| Fast Water setup 0.00 ( 0.05% of Total) +| Calc gb radii 0.00 (21.81% of Gen B) +| Calc gb diag 0.01 (36.40% of Gen B) +| Calc gb off-diag 0.01 (41.68% of Gen B) +| Other 0.00 ( 0.11% of Gen B) +| Gen Born time 0.01 (100.0% of Nonbo) +| Nonbond force 0.01 (90.95% of Force) +| Bond/Angle/Dihedral 0.00 ( 7.05% of Force) +| Other 0.00 ( 2.00% of Force) +| Force time 0.02 (84.01% of Runmd) +| Shake time 0.00 ( 0.37% of Runmd) +| Verlet update time 0.00 (11.95% of Runmd) +| Other 0.00 ( 3.67% of Runmd) +| Runmd Time 0.02 (77.08% of Total) +| Other 0.01 (21.37% of Total) +| Total time 0.02 (99.74% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 -| Job began at 17:03:35.162 on 02/06/2008 -| Setup done at 17:03:35.167 on 02/06/2008 -| Run done at 17:03:35.179 on 02/06/2008 +| Job began at 16:13:58.759 on 10/14/2009 +| Setup done at 16:13:58.765 on 10/14/2009 +| Run done at 16:13:58.783 on 10/14/2009 | wallclock() was called 250 times --- test/plane_plane_restraint/mdout.dinucAU_pln.save 2008-03-17 22:15:07.000000000 -0400 +++ test/plane_plane_restraint/mdout.dinucAU_pln.save 2009-10-14 17:54:10.000000000 -0400 @@ -3,7 +3,7 @@ Amber 10 SANDER 2008 ------------------------------------------------------- -| Run on 02/06/2008 at 17:03:35 +| Run on 10/14/2009 at 16:13:50 [-O]verwriting output File Assignments: @@ -17,9 +17,12 @@ | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo +| MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip +|INPTRA: inptraj +| Here is the input file: @@ -58,12 +61,12 @@ | Memory Use Allocated | Real 3524 -| Hollerith 370 +| Hollerith 187 | Integer 23425 | Max Pairs 1 | nblistReal 0 | nblist Int 0 -| Total 120 kbytes +| Total 119 kbytes | Duplicated 0 dihedrals | Duplicated 0 dihedrals @@ -168,8 +171,8 @@ | NDFMIN = 152. NUM_NOSHAKE = 0 CORRECTED RNDFP = 152. | TOTAL # of degrees of freedom (RNDF) = 152. - NSTEP = 1 TIME(PS) = 0.011 TEMP(K) = 204.88 PRESS = 0.0 - Etot = -28.4025 EKtot = 30.9427 EPtot = -59.3452 + NSTEP = 1 TIME(PS) = 0.011 TEMP(K) = 204.89 PRESS = 0.0 + Etot = -28.4010 EKtot = 30.9442 EPtot = -59.3452 BOND = 5.5498 ANGLE = 43.4372 DIHED = 37.8640 1-4 NB = 18.2261 1-4 EEL = -9.8751 VDWAALS = -2.1293 EELEC = -96.1686 EGB = -65.1442 RESTRAINT = 8.8951 @@ -181,137 +184,137 @@ =============================================================================== NSTEP = 2 TIME(PS) = 0.012 TEMP(K) = 147.42 PRESS = 0.0 - Etot = -28.0315 EKtot = 22.2646 EPtot = -50.2961 - BOND = 5.2221 ANGLE = 51.9125 DIHED = 38.0225 - 1-4 NB = 18.6234 1-4 EEL = -10.3122 VDWAALS = -1.2448 - EELEC = -96.1971 EGB = -65.2226 RESTRAINT = 8.9000 - EAMBER (non-restraint) = -59.1962 + Etot = -28.0290 EKtot = 22.2643 EPtot = -50.2933 + BOND = 5.2230 ANGLE = 51.9127 DIHED = 38.0225 + 1-4 NB = 18.6245 1-4 EEL = -10.3136 VDWAALS = -1.2456 + EELEC = -96.1951 EGB = -65.2227 RESTRAINT = 8.9011 + EAMBER (non-restraint) = -59.1944 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.043 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 7.044 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.857 =============================================================================== - NSTEP = 3 TIME(PS) = 0.013 TEMP(K) = 129.05 PRESS = 0.0 - Etot = -27.6894 EKtot = 19.4904 EPtot = -47.1798 - BOND = 4.8340 ANGLE = 55.2334 DIHED = 38.1413 - 1-4 NB = 18.6654 1-4 EEL = -10.6741 VDWAALS = -0.7589 - EELEC = -96.1824 EGB = -65.3346 RESTRAINT = 8.8960 - EAMBER (non-restraint) = -56.0758 + NSTEP = 3 TIME(PS) = 0.013 TEMP(K) = 128.99 PRESS = 0.0 + Etot = -27.6899 EKtot = 19.4807 EPtot = -47.1707 + BOND = 4.8375 ANGLE = 55.2340 DIHED = 38.1410 + 1-4 NB = 18.6687 1-4 EEL = -10.6781 VDWAALS = -0.7615 + EELEC = -96.1764 EGB = -65.3351 RESTRAINT = 8.8992 + EAMBER (non-restraint) = -56.0699 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.040 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 7.044 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.856 =============================================================================== - NSTEP = 4 TIME(PS) = 0.014 TEMP(K) = 153.33 PRESS = 0.0 - Etot = -27.3830 EKtot = 23.1569 EPtot = -50.5398 - BOND = 4.8000 ANGLE = 52.6528 DIHED = 38.2103 - 1-4 NB = 18.2587 1-4 EEL = -10.9750 VDWAALS = -0.7813 - EELEC = -96.1078 EGB = -65.4804 RESTRAINT = 8.8829 - EAMBER (non-restraint) = -59.4227 + NSTEP = 4 TIME(PS) = 0.014 TEMP(K) = 153.16 PRESS = 0.0 + Etot = -27.3904 EKtot = 23.1309 EPtot = -50.5214 + BOND = 4.8077 ANGLE = 52.6542 DIHED = 38.2097 + 1-4 NB = 18.2648 1-4 EEL = -10.9827 VDWAALS = -0.7870 + EELEC = -96.0960 EGB = -65.4813 RESTRAINT = 8.8892 + EAMBER (non-restraint) = -59.4106 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.033 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 7.040 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.850 =============================================================================== - NSTEP = 5 TIME(PS) = 0.015 TEMP(K) = 211.05 PRESS = 0.0 - Etot = -27.1007 EKtot = 31.8736 EPtot = -58.9744 - BOND = 5.5491 ANGLE = 45.0934 DIHED = 38.2411 - 1-4 NB = 17.4838 1-4 EEL = -11.2441 VDWAALS = -1.3525 - EELEC = -95.9465 EGB = -65.6596 RESTRAINT = 8.8610 - EAMBER (non-restraint) = -67.8354 + NSTEP = 5 TIME(PS) = 0.015 TEMP(K) = 210.73 PRESS = 0.0 + Etot = -27.1193 EKtot = 31.8264 EPtot = -58.9457 + BOND = 5.5613 ANGLE = 45.0953 DIHED = 38.2402 + 1-4 NB = 17.4933 1-4 EEL = -11.2563 VDWAALS = -1.3626 + EELEC = -95.9271 EGB = -65.6612 RESTRAINT = 8.8714 + EAMBER (non-restraint) = -67.8171 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.022 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 7.032 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.839 =============================================================================== - NSTEP = 6 TIME(PS) = 0.016 TEMP(K) = 283.13 PRESS = 0.0 - Etot = -26.8050 EKtot = 42.7602 EPtot = -69.5652 - BOND = 7.3791 ANGLE = 34.8549 DIHED = 38.2622 - 1-4 NB = 16.5307 1-4 EEL = -11.5190 VDWAALS = -2.3695 - EELEC = -95.6699 EGB = -65.8645 RESTRAINT = 8.8309 - EAMBER (non-restraint) = -78.3961 + NSTEP = 6 TIME(PS) = 0.016 TEMP(K) = 282.66 PRESS = 0.0 + Etot = -26.8387 EKtot = 42.6898 EPtot = -69.5285 + BOND = 7.3942 ANGLE = 34.8565 DIHED = 38.2609 + 1-4 NB = 16.5438 1-4 EEL = -11.5359 VDWAALS = -2.3857 + EELEC = -95.6415 EGB = -65.8670 RESTRAINT = 8.8461 + EAMBER (non-restraint) = -78.3746 ------------------------------------------------------------------------------ - NMR restraints: Bond = 7.007 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 7.022 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.824 =============================================================================== - NSTEP = 7 TIME(PS) = 0.017 TEMP(K) = 346.76 PRESS = 0.0 - Etot = -26.4285 EKtot = 52.3696 EPtot = -78.7981 - BOND = 10.3176 ANGLE = 24.9349 DIHED = 38.3076 - 1-4 NB = 15.5814 1-4 EEL = -11.8380 VDWAALS = -3.5591 - EELEC = -95.2597 EGB = -66.0764 RESTRAINT = 8.7936 - EAMBER (non-restraint) = -87.5916 + NSTEP = 7 TIME(PS) = 0.017 TEMP(K) = 346.15 PRESS = 0.0 + Etot = -26.4812 EKtot = 52.2779 EPtot = -78.7592 + BOND = 10.3322 ANGLE = 24.9345 DIHED = 38.3059 + 1-4 NB = 15.5979 1-4 EEL = -11.8595 VDWAALS = -3.5835 + EELEC = -95.2212 EGB = -66.0798 RESTRAINT = 8.8143 + EAMBER (non-restraint) = -87.5734 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.988 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 7.008 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.806 =============================================================================== - NSTEP = 8 TIME(PS) = 0.018 TEMP(K) = 383.33 PRESS = 0.0 - Etot = -25.9142 EKtot = 57.8936 EPtot = -83.8078 - BOND = 14.0379 ANGLE = 18.0917 DIHED = 38.4008 - 1-4 NB = 14.7418 1-4 EEL = -12.2324 VDWAALS = -4.6089 - EELEC = -94.7184 EGB = -66.2703 RESTRAINT = 8.7500 - EAMBER (non-restraint) = -92.5578 + NSTEP = 8 TIME(PS) = 0.018 TEMP(K) = 382.62 PRESS = 0.0 + Etot = -25.9891 EKtot = 57.7859 EPtot = -83.7750 + BOND = 14.0473 ANGLE = 18.0866 DIHED = 38.3986 + 1-4 NB = 14.7612 1-4 EEL = -12.2582 VDWAALS = -4.6438 + EELEC = -94.6688 EGB = -66.2747 RESTRAINT = 8.7768 + EAMBER (non-restraint) = -92.5518 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.965 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 6.992 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.785 =============================================================================== - NSTEP = 9 TIME(PS) = 0.019 TEMP(K) = 384.86 PRESS = 0.0 - Etot = -25.2646 EKtot = 58.1241 EPtot = -83.3887 - BOND = 17.8864 ANGLE = 15.9954 DIHED = 38.5418 - 1-4 NB = 14.0425 1-4 EEL = -12.7219 VDWAALS = -5.3438 - EELEC = -94.0703 EGB = -66.4205 RESTRAINT = 8.7016 - EAMBER (non-restraint) = -92.0904 + NSTEP = 9 TIME(PS) = 0.019 TEMP(K) = 384.09 PRESS = 0.0 + Etot = -25.3642 EKtot = 58.0072 EPtot = -83.3714 + BOND = 17.8859 ANGLE = 15.9822 DIHED = 38.5389 + 1-4 NB = 14.0643 1-4 EEL = -12.7512 VDWAALS = -5.3913 + EELEC = -94.0090 EGB = -66.4261 RESTRAINT = 8.7350 + EAMBER (non-restraint) = -92.1064 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.940 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 6.974 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.761 =============================================================================== - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 355.50 PRESS = 0.0 - Etot = -24.5364 EKtot = 53.6903 EPtot = -78.2267 - BOND = 21.0499 ANGLE = 18.8212 DIHED = 38.7093 - 1-4 NB = 13.4715 1-4 EEL = -13.3134 VDWAALS = -5.7610 - EELEC = -93.3547 EGB = -66.4992 RESTRAINT = 8.6498 - EAMBER (non-restraint) = -86.8765 + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 354.71 PRESS = 0.0 + Etot = -24.6622 EKtot = 53.5703 EPtot = -78.2325 + BOND = 21.0364 ANGLE = 18.7966 DIHED = 38.7058 + 1-4 NB = 13.4949 1-4 EEL = -13.3454 VDWAALS = -5.8236 + EELEC = -93.2813 EGB = -66.5060 RESTRAINT = 8.6900 + EAMBER (non-restraint) = -86.9226 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.914 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 6.954 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.736 =============================================================================== A V E R A G E S O V E R 10 S T E P S - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 259.93 PRESS = 0.0 - Etot = -26.7556 EKtot = 39.2566 EPtot = -66.0122 - BOND = 9.6626 ANGLE = 36.1027 DIHED = 38.2701 - 1-4 NB = 16.5625 1-4 EEL = -11.4705 VDWAALS = -2.7909 - EELEC = -95.3676 EGB = -65.7972 RESTRAINT = 8.8161 - EAMBER (non-restraint) = -74.8283 + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 259.54 PRESS = 0.0 + Etot = -26.7965 EKtot = 39.1978 EPtot = -65.9943 + BOND = 9.6675 ANGLE = 36.0990 DIHED = 38.2688 + 1-4 NB = 16.5739 1-4 EEL = -11.4856 VDWAALS = -2.8114 + EELEC = -95.3385 EGB = -65.7998 RESTRAINT = 8.8318 + EAMBER (non-restraint) = -74.8261 ------------------------------------------------------------------------------ - NMR restraints: Bond = 6.914 Angle = 0.000 Torsion = 0.000 + NMR restraints: Bond = 6.954 Angle = 0.000 Torsion = 0.000 : Plane-Point = 0.000 Plane-Plane = 1.736 =============================================================================== R M S F L U C T U A T I O N S - NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 97.27 PRESS = 0.0 - Etot = 1.1701 EKtot = 14.6906 EPtot = 13.7075 - BOND = 5.6798 ANGLE = 14.7584 DIHED = 0.2308 - 1-4 NB = 1.8801 1-4 EEL = 1.0246 VDWAALS = 1.8021 - EELEC = 0.9558 EGB = 0.4772 RESTRAINT = 0.0848 - EAMBER (non-restraint) = 13.6226 + NSTEP = 10 TIME(PS) = 0.020 TEMP(K) = 96.98 PRESS = 0.0 + Etot = 1.1273 EKtot = 14.6468 EPtot = 13.7021 + BOND = 5.6754 ANGLE = 14.7641 DIHED = 0.2297 + 1-4 NB = 1.8720 1-4 EEL = 1.0356 VDWAALS = 1.8215 + EELEC = 0.9797 EGB = 0.4795 RESTRAINT = 0.0716 + EAMBER (non-restraint) = 13.6306 ------------------------------------------------------------------------------ @@ -329,39 +332,38 @@ First atom Last atom curr. value target deviation penalty ------------------------------------------------------------------------------ N9 RAN 1 -- N1 RUN 2: 166.327 180.000 13.673 1.709 n - *N3 RAN 1 -- *C2 RUN 2: 6.515 5.000 1.515 6.887 d 0: 0 - Total distance penalty: 6.887 + *N3 RAN 1 -- *C2 RUN 2: 6.520 5.000 1.520 6.935 d 0: 0 + Total distance penalty: 6.935 Total plane-plane angle penalty: 1.709 | RMS deviation from ideal bonds : 0.0391 -| RMS deviation from ideal angles: 3.375 +| RMS deviation from ideal angles: 3.374 ------------------------------------------------------------------------------ -------------------------------------------------------------------------------- 5. TIMINGS -------------------------------------------------------------------------------- -| Read coords time 0.00 ( 2.19% of Total) -| Fast Water setup 0.00 ( 0.08% of Total) -| Calc gb radii 0.00 (26.09% of Gen B) -| Calc gb diag 0.00 (36.16% of Gen B) -| Calc gb off-diag 0.00 (36.97% of Gen B) -| Other 0.00 ( 0.78% of Gen B) -| Gen Born time 0.01 (99.87% of Nonbo) -| IPS excludes 0.00 ( 0.13% of Nonbo) -| Nonbond force 0.01 (81.90% of Force) -| Bond/Angle/Dihedral 0.00 (13.78% of Force) -| Other 0.00 ( 4.31% of Force) -| Force time 0.01 (72.41% of Runmd) -| Shake time 0.00 ( 0.60% of Runmd) -| Verlet update time 0.00 (20.96% of Runmd) -| Other 0.00 ( 6.02% of Runmd) -| Runmd Time 0.01 (68.69% of Total) -| Other 0.00 (29.04% of Total) -| Total time 0.02 (99.56% of ALL ) +| Read coords time 0.00 ( 0.21% of Total) +| Calc gb radii 0.00 (21.87% of Gen B) +| Calc gb diag 0.01 (35.63% of Gen B) +| Calc gb off-diag 0.01 (42.38% of Gen B) +| Other 0.00 ( 0.12% of Gen B) +| Gen Born time 0.01 (100.0% of Nonbo) +| IPS excludes 0.00 ( 0.01% of Nonbo) +| Nonbond force 0.01 (90.99% of Force) +| Bond/Angle/Dihedral 0.00 ( 6.99% of Force) +| Other 0.00 ( 2.02% of Force) +| Force time 0.02 (18.06% of Runmd) +| Shake time 0.00 ( 0.07% of Runmd) +| Verlet update time 0.00 ( 2.63% of Runmd) +| Other 0.07 (79.23% of Runmd) +| Runmd Time 0.09 (32.99% of Total) +| Other 0.17 (66.79% of Total) +| Total time 0.26 (88.15% of ALL ) | Highest rstack allocated: 0 | Highest istack allocated: 0 -| Job began at 17:03:35.282 on 02/06/2008 -| Setup done at 17:03:35.288 on 02/06/2008 -| Run done at 17:03:35.299 on 02/06/2008 +| Job began at 16:13:50.135 on 10/14/2009 +| Setup done at 16:13:50.369 on 10/14/2009 +| Run done at 16:13:50.455 on 10/14/2009 | wallclock() was called 250 times --- src/pmemd/src/nmr_lib.fpp 2008-03-28 17:20:54.000000000 -0400 +++ src/pmemd/src/nmr_lib.fpp 2009-11-04 13:25:08.000000000 -0500 @@ -1741,7 +1741,7 @@ jx = nmrat(iat, i) do m = 1, 3 - frc(jx + m) = frc(jx + m) - dfr(jatm + 1) + frc(jx + m) = frc(jx + m) - dfr(jatm + m) end do end if ---------------------------------------------------------------------------- Temporary workarounds: None