1 2 3 4 5 n w A R G O S Author T.P.Straatsma 6 High Performance Computational Chemistry 7 Environmental Molecular Sciences Laboratory 8 Pacific Northwest National Laboratory 9 10 Copyright 1995, 1996, 1997 11 Pacific Northwest National Laboratory 12 Environmental Molecular Sciences Laboratory 13 14 This is a parallelized version of the ARGOS molecular simulation software 15 Copyright 1989,1995 T.P.Straatsma, and provided under license 16 17 MOLECULAR DYNAMICS SIMULATION 18 19 Title input NWChem:nwARGOS input Creation date 97/06/25 20 Creation time 14:42:17 21 22 Title topology Argos benchmark job ab02 Creation date 93/01/28 23 Myoglobin in SPC/E water Creation time 16:15:22 24 25 Title coordinates nwARGOS example MD run Creation date Jun 18 96 26 Aqueous solution of myoglobin Creation time 20:49:13 27 1000 steps MD 28 Today's date 97/06/25 29 Today's time 14:42:17 30 31 32 33 34 FORCE FIELD gromos 35 36 37 38 39 40 ATOMIC DATA 97/06/25 14:42:22 41 42 Number Type Mass Type Mass Type Mass 43 a.m.u. a.m.u. a.m.u. 44 45 1 OW 15.99940 OW 15.99940 OW 15.99940 46 2 HW 1.00800 HW 1.00800 HW 1.00800 47 3 N 14.00670 N 14.00670 N 14.00670 48 4 H 1.00800 H 1.00800 H 1.00800 49 5 CH1 13.01900 CH1 13.01900 CH1 13.01900 50 6 CH3 15.03500 CH3 15.03500 CH3 15.03500 51 7 C 12.01100 C 12.01100 C 12.01100 52 8 O 15.99940 O 15.99940 O 15.99940 53 9 CH2 14.02700 CH2 14.02700 CH2 14.02700 54 10 NEE 14.00670 NEE 14.00670 NEE 14.00670 55 11 NZ 14.00670 NZ 14.00670 NZ 14.00670 56 12 NT 14.00670 NT 14.00670 NT 14.00670 57 13 OM 15.99940 OM 15.99940 OM 15.99940 58 14 OA 15.99940 OA 15.99940 OA 15.99940 59 15 HO 1.00800 HO 1.00800 HO 1.00800 60 16 CB 12.01100 CB 12.01100 CB 12.01100 61 17 NR5* 14.00670 NR5* 14.00670 NR5* 14.00670 62 18 CR51 13.01900 CR51 13.01900 CR51 13.01900 63 19 NR5 14.00670 NR5 14.00670 NR5 14.00670 64 20 NL 14.00670 NL 14.00670 NL 14.00670 65 21 S 32.06000 S 32.06000 S 32.06000 66 22 CR61 13.01900 CR61 13.01900 CR61 13.01900 67 23 FE 55.84700 FE 55.84700 FE 55.84700 68 24 NP 14.00670 NP 14.00670 NP 14.00670 69 70 71 GENERAL SYSTEM INFORMATION 97/06/25 14:42:22 72 73 Solvent Solute Total 74 75 Number of atoms 9384 1530 10914 76 Number of centers 9384 1530 10914 77 Number of molecules 3128 1 3129 78 Number of dynamical atoms 9384 1530 10914 79 Number of non dynamical atoms 0 0 0 80 Number of bonds 3 1566 1569 81 Number of constraints 3 270 273 82 Number of angles 0 2269 2269 83 Number of proper dihedral angles 0 832 832 84 Number of improper dihedral angles 0 777 777 85 Number of third neighbor atom pairs 0 2736 2736 86 Number of non-bonded intramolecular atom pairs 0 1169685 1169685 87 Number of excluded atom pairs 6574 6574 88 Number of degrees of freedom 18768.000 4320.000 23088 89 90 91 92 Special solute bonded interactions 93 94 Constr 95 96 Number of bonds 270 97 Number of angles 0 98 Number of proper dihedrals 0 99 Number of improper dihedrals 0 100 101 Dimension of the box in nm 4.956378 4.956378 4.956378 102 103 Tolerance SHAKE solvent .001000 104 solute .001000 105 106 Cut off radii in nm short range long range 107 neutral neutral charged neutral neutral charged 108 neutral charged charged neutral charged charged 109 solvent-solvent 1.600000 1.600000 110 solute -solvent 1.600000 1.600000 1.600000 1.600000 111 solute -solute 1.600000 1.600000 1.600000 1.600000 1.600000 1.600000 112 qmmm boundary .900000 113 114 Coulombic third neighbor scaling factor Coulombic interactions 1.000000 115 Relative dielectric constant 1.000000 116 117 Solute - solute pairlist based on group distance 118 119 120 Periodic boundary conditions applied 121 122 123 Leap frog integration algorithm 124 125 126 127 MOLECULAR DYNAMICS PARAMETERS 97/06/25 14:42:22 128 129 Sequence number 0 Time .00000 ps 130 Calculation type 1 Time step .00100 ps 131 Number of equilibration steps 0 132 Number of data gathering steps 1000 133 134 Frequency output statistics 1000 135 Frequency updating restart file 0 136 Frequency step output 100 137 Frequency recording coordinates 0 138 Frequency recording solute coordinates 0 139 Frequency recording properties 0 140 Frequency recording velocities 0 141 Frequency recording solute velocities 0 142 Frequency centering box 0 143 Frequency box center of mass motion removal 0 144 Frequency solvent-solvent pairlist 1 145 Frequency solvent-solvent long range forces 1 146 Frequency solvent-solute pairlist 1 147 Frequency solvent-solute long range forces 1 148 Frequency solute-solute pairlist 1 149 Frequency solute-solute long range forces 1 150 No switching function used 151 152 Adiabatic isochoric (NVE) ensemble 153 154 155 156 CALCULATION TYPE 157 158 This is an initial job with 0 equilibration and 1000 data gathering steps 159 160 161 DIMENSIONS AT INITIALIZATION 97/06/25 14:42:22 162 163 MAT : max number of atom types 24 MAXW : max length of work arrays 2736 164 MWM : max number of solvent molecules 475 MSM : max number of solute molecules 5 165 MWA : max number of solvent atoms 3 MSA : max number of solute atoms 1422 166 MWB : max number of solvent bonds 3 MSB : max number of solute bonds 1566 167 MWH : max number of solvent angles 1 MSH : max number of solute angles 2269 168 MWD : max number of solvent proper dihedrals 1 MSD : max number of solute proper dihedrals 1664 169 MWO : max number of solvent improper dihedrals 1 MSO : max number of solute improper dihedrals 777 170 MSG : max number of solute groups 948 171 MSS : max number of solute segments 154 172 MPN : max length of property arrays 172 173 MGC : max number RDF contributions 1 SMALL : small real number 1.00E-12 174 MGR : max number RDF's 1 TINY : tiny real number 1.00E-14 175 MGL : max length RDF's 1 SIL : sin(dihedral) algorithm change .001000 176 MSHITW: max number solvent SHAKE iterations 100 MSHITS: max number solute SHAKE iterations 100 177 178 179 SPACIAL DECOMPOSITION INFORMATION 97/06/25 14:42:22 180 181 182 Largest number of sub-boxes in one dimension 6 183 Largest number of sub-boxes per node 1 184 185 Number of additional sub-boxes per node 6 186 187 Load balancing through box-pair redistribution 188 189 Number of nodes 54 divided 3 x 3 x 6 190 Number of boxes 54 divided 3 x 3 x 6 191 192 Initial distribution of box-box pairs 193 194 Node Pairs Node Pairs Node Pairs Node Pairs Node Pairs Node Pairs Node Pairs Node Pairs 195 0 21 1 22 2 23 3 24 4 23 5 22 6 23 7 24 196 8 25 9 21 10 22 11 23 12 24 13 23 14 22 15 23 197 16 24 17 25 18 21 19 22 20 23 21 24 22 23 23 22 198 24 23 25 24 26 25 27 21 28 22 29 23 30 24 31 23 199 32 22 33 23 34 24 35 25 36 21 37 22 38 23 39 24 200 40 23 41 22 42 23 43 24 44 25 45 21 46 22 47 23 201 48 24 49 23 50 22 51 23 52 24 53 25 202 203 Initial number of solvent molecules 204 205 Node nwm Node nwm Node nwm Node nwm Node nwm Node nwm Node nwm Node nwm 206 0 75 1 67 2 77 3 71 4 71 5 77 6 72 7 76 207 8 72 9 78 10 60 11 72 12 64 13 62 14 65 15 67 208 16 52 17 60 18 69 19 52 20 68 21 30 22 4 23 49 209 24 39 25 17 26 40 27 66 28 38 29 66 30 37 31 0 210 32 36 33 24 34 8 35 35 36 71 37 68 38 72 39 58 211 40 42 41 57 42 57 43 56 44 71 45 72 46 76 47 72 212 48 72 49 69 50 78 51 77 52 71 53 73 213 214 Initial number of solute atoms 215 216 Node nsa Node nsa Node nsa Node nsa Node nsa Node nsa Node nsa Node nsa 217 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 218 8 0 9 0 10 0 11 0 12 0 13 9 14 0 15 0 219 16 26 17 45 18 0 19 21 20 0 21 106 22 172 23 29 220 24 78 25 109 26 64 27 0 28 76 29 13 30 41 31 129 221 32 87 33 86 34 176 35 84 36 0 37 0 38 0 39 23 222 40 62 41 17 42 47 43 22 44 8 45 0 46 0 47 0 223 48 0 49 0 50 0 51 0 52 0 53 0 224 225 MOLECULAR DYNAMICS TIME STEP INFORMATION 97/06/25 14:43:19 226 227 Time Temp Pres Volume Tscal Pscal U(Cou) U(L-J) U(pot) U(kin) U(tot) 228 ps K Pa nm**3 kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol 229 U(bnd) U(ang) U(dih) Ui(Cou) Ui(L-J) Uw(Cou) Uw(L-J) U(kin) U(pot) U(tot) 230 kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol kJ/mol 231 232 .10000 332.17-6.36E+07 121.757 1.0000 1.0000-1.7946E+05 1.6844E+04-1.4095E+05 3.1882E+04-1.0906E+05 0 0 233 Solvent .000 .000 .000 .000 .000 -47.861 7.559 8.833 -38.171 -29.338 234 Solute 1 939.027 2608.543 1796.303 -11564.848 -5665.525 -18187.910 -1135.086 4253.539 -21547.998 -17294.459 235 .20000 336.46-3.90E+07 121.757 1.0000 1.0000-1.7889E+05 1.6457E+04-1.4101E+05 3.2294E+04-1.0871E+05 0 0 236 Solvent .000 .000 .000 .000 .000 -47.535 7.330 8.884 -38.132 -29.248 237 Solute 1 781.967 2565.413 1752.637 -11416.048 -5570.207 -18786.648 -901.867 4504.230 -21730.495 -17226.266 238 .30000 332.92-4.48E+06 121.757 1.0000 1.0000-1.7909E+05 1.7053E+04-1.4041E+05 3.1954E+04-1.0846E+05 0 0 239 Solvent .000 .000 .000 .000 .000 -47.627 7.516 8.820 -38.039 -29.219 240 Solute 1 927.347 2664.218 1704.837 -11250.482 -5624.803 -18858.919 -831.818 4363.844 -21424.250 -17060.406 241 .40000 335.06-2.75E+07 121.757 1.0000 1.0000-1.7956E+05 1.7173E+04-1.4069E+05 3.2160E+04-1.0853E+05 0 0 242 Solvent .000 .000 .000 .000 .000 -47.996 7.635 8.900 -38.182 -29.282 243 Solute 1 988.356 2625.766 1756.212 -11461.483 -5650.786 -17967.356 -1059.088 4321.299 -21255.157 -16933.857 244 .50000 331.66-7.90E+06 121.757 1.0000 1.0000-1.7821E+05 1.6793E+04-1.3985E+05 3.1833E+04-1.0802E+05 0 0 245 Solvent .000 .000 .000 .000 .000 -47.416 7.337 8.757 -37.954 -29.198 246 Solute 1 919.961 2537.279 1782.168 -11331.470 -5356.677 -18565.989 -801.356 4442.971 -21132.412 -16689.441 247 .60000 334.86 7.59E+05 121.757 1.0000 1.0000-1.7931E+05 1.7174E+04-1.4048E+05 3.2141E+04-1.0834E+05 0 0 248 Solvent .000 .000 .000 .000 .000 -47.729 7.540 8.860 -38.034 -29.173 249 Solute 1 933.235 2649.026 1742.456 -11804.793 -5442.451 -18205.949 -967.542 4426.270 -21509.272 -17083.002 250 .70000 336.52 3.19E+07 121.757 1.0000 1.0000-1.7914E+05 1.7278E+04-1.4006E+05 3.2300E+04-1.0776E+05 0 0 251 Solvent .000 .000 .000 .000 .000 -47.760 7.578 8.855 -38.072 -29.217 252 Solute 1 992.636 2685.718 1795.305 -11120.995 -5597.400 -18626.087 -828.889 4600.818 -20972.224 -16371.406 253 .80000 337.48 2.93E+07 121.757 1.0000 1.0000-1.7927E+05 1.7215E+04-1.4004E+05 3.2392E+04-1.0765E+05 0 0 254 Solvent .000 .000 .000 .000 .000 -47.780 7.581 8.916 -38.074 -29.159 255 Solute 1 1086.162 2783.029 1817.076 -11328.813 -5623.380 -18489.424 -873.418 4503.977 -20947.347 -16443.371 256 .90000 337.75-6.52E+07 121.757 1.0000 1.0000-1.7789E+05 1.5921E+04-1.4015E+05 3.2418E+04-1.0774E+05 0 0 257 Solvent .000 .000 .000 .000 .000 -47.272 7.164 8.904 -38.028 -29.124 258 Solute 1 995.222 2736.853 1754.589 -11332.176 -5537.251 -18689.313 -952.689 4567.059 -21203.762 -16636.704 259 1.00000 334.48-1.62E+07 121.757 1.0000 1.0000-1.7848E+05 1.6616E+04-1.4014E+05 3.2104E+04-1.0804E+05 0 0 260 Solvent .000 .000 .000 .000 .000 -47.404 7.408 8.814 -37.895 -29.081 261 Solute 1 985.932 2675.865 1732.150 -11678.865 -5561.353 -18521.778 -995.396 4533.442 -21604.857 -17071.415 262 263 MOLECULAR DYNAMICS STATISTICAL INFORMATION 97/06/25 14:50:35 264 265 Statistics over last 1000 steps Statistics over last 1000 steps 266 Average RMS fluct Drift/ps Average RMS fluct Drift/ps 267 268 Number solvent-solvent interactions 7.45828E+05 5.92317E+02 -1.67639E+03 7.45828E+05 5.92317E+02 -1.67639E+03 269 Number solvent-solute interactions 2.78473E+05 1.12283E+03 3.68981E+03 2.78473E+05 1.12283E+03 3.68981E+03 270 Number solute-solute interactions 4.13644E+05 1.50202E+03 -3.78419E+03 4.13644E+05 1.50202E+03 -3.78419E+03 271 Number solvent-solvent cycles 5.49340E+01 1.09346E+00 2.28082E+00 5.49340E+01 1.09346E+00 2.28082E+00 272 Number solvent-solute cycles 5.40010E+01 3.16070E-02 1.57800E-03 5.40010E+01 3.16070E-02 1.57800E-03 273 Number solute-solute cycles 3.01870E+01 9.96008E-01 2.16702E-01 3.01870E+01 9.96008E-01 2.16702E-01 274 Number of available solvent molecules 3.19098E+02 2.04215E+00 -1.65756E-01 3.19098E+02 2.04215E+00 -1.65756E-01 275 Number of available solute atoms 1.06457E+03 8.95172E+00 6.86595E+00 1.06457E+03 8.95172E+00 6.86595E+00 276 Number of solvent SHAKE iterations 2.24640E+01 4.98702E-01 2.58576E-01 2.24640E+01 4.98702E-01 2.58576E-01 277 Number of solute SHAKE iterations 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 278 Box length X 4.95638E+00 9.42477E-07 4.15287E-13 4.95638E+00 9.42477E-07 4.15287E-13 nm 279 Box length Y 4.95638E+00 9.42477E-07 4.15287E-13 4.95638E+00 9.42477E-07 4.15287E-13 nm 280 Box length Z 4.95638E+00 9.42477E-07 4.15287E-13 4.95638E+00 9.42477E-07 4.15287E-13 nm 281 Volume 1.21757E+02 0.00000E+00 -1.40777E-11 1.21757E+02 0.00000E+00 -1.40777E-11 nm**3 282 Mass density 1.01157E+03 3.91396E-05 6.30012E-11 1.01157E+03 3.91396E-05 6.30012E-11 kg/m**3 283 Pressure -1.61917E+07 2.62281E+07 -1.07901E+07 -1.61917E+07 2.62281E+07 -1.07901E+07 Pa 284 Temperature 3.35102E+02 3.71331E+00 7.34172E+00 3.35102E+02 3.71331E+00 7.34172E+00 K 285 Temperature (corrected) 3.34616E+02 3.71913E+00 7.37775E+00 3.34616E+02 3.71913E+00 7.37775E+00 K 286 Temperature solvent 3.55117E+02 3.66535E+00 4.61331E+00 3.55117E+02 3.66535E+00 4.61331E+00 K 287 Temperature solvent (corrected) 3.54523E+02 3.66503E+00 4.64461E+00 3.54523E+02 3.66503E+00 4.64461E+00 K 288 Temperature solute 2.48149E+02 7.19282E+00 1.91951E+01 2.48149E+02 7.19282E+00 1.91951E+01 K 289 Temperature solute (corrected) 2.48131E+02 7.20424E+00 1.92517E+01 2.48131E+02 7.20424E+00 1.92517E+01 K 290 Temperature translations 1.45046E+02 2.47550E+00 4.83972E+00 1.45046E+02 2.47550E+00 4.83972E+00 K 291 Temperature rotations 1.89570E+02 2.12486E+00 2.53803E+00 1.89570E+02 2.12486E+00 2.53803E+00 K 292 Energy Coulombic -1.79058E+05 5.42659E+02 7.24155E+02 -1.79058E+05 5.42659E+02 7.24155E+02 kJ/mol 293 Energy Lennard-Jones 1.69194E+04 3.24834E+02 -2.31419E+02 1.69194E+04 3.24834E+02 -2.31419E+02 kJ/mol 294 Energy potential -1.40450E+05 3.92093E+02 7.54823E+02 -1.40450E+05 3.92093E+02 7.54823E+02 kJ/mol 295 Energy kinetic 3.21169E+04 3.56968E+02 7.08128E+02 3.21169E+04 3.56968E+02 7.08128E+02 kJ/mol 296 Energy kinetic translations 1.39217E+04 2.37602E+02 4.64523E+02 1.39217E+04 2.37602E+02 4.64523E+02 kJ/mol 297 Energy kinetic rotations 1.81952E+04 2.03948E+02 2.43604E+02 1.81952E+04 2.03948E+02 2.43604E+02 kJ/mol 298 Energy kinetic translations * virial 4.37118E+08 8.30692E+07 6.19927E+07 4.37118E+08 8.30692E+07 6.19927E+07 (kJ/mol)**2 299 Energy kinetic rotations * virial 5.71182E+08 1.07928E+08 7.08407E+07 5.71182E+08 1.07928E+08 7.08407E+07 (kJ/mol)**2 300 Energy total -1.08333E+05 4.64125E+02 1.46295E+03 -1.08333E+05 4.64125E+02 1.46295E+03 kJ/mol 301 Virial total 8.47181E+05 1.57633E+05 9.36483E+04 8.47181E+05 1.57633E+05 9.36483E+04 kJ/mol 302 pV total -1.18722E+03 1.92311E+03 -7.91154E+02 -1.18722E+03 1.92311E+03 -7.91154E+02 kJ/mol 303 Enthalpy -1.09520E+05 1.95611E+03 6.71797E+02 -1.09520E+05 1.95611E+03 6.71797E+02 kJ/mol 304 System dipole moment 7.32765E+02 1.09900E+02 -2.03556E+02 7.32765E+02 1.09900E+02 -2.03556E+02 e30 C m 305 Energy solvent inter Coulombic -1.49110E+05 5.86315E+02 8.16877E+02 -1.49110E+05 5.86315E+02 8.16877E+02 kJ/mol 306 Energy solvent inter Lennard-Jones 2.34487E+04 3.60506E+02 -3.23320E+02 2.34487E+04 3.60506E+02 -3.23320E+02 kJ/mol 307 Energy solvent kinetic translations 1.39176E+04 2.37857E+02 4.65822E+02 1.39176E+04 2.37857E+02 4.65822E+02 kJ/mol 308 Energy solvent kinetic 2.76607E+04 2.85954E+02 3.62384E+02 2.76607E+04 2.85954E+02 3.62384E+02 kJ/mol 309 Energy solvent potential -1.19059E+05 3.19781E+02 4.41915E+02 -1.19059E+05 3.19781E+02 4.41915E+02 kJ/mol 310 Energy solvent total -9.13987E+04 2.56671E+02 8.04299E+02 -9.13987E+04 2.56671E+02 8.04299E+02 kJ/mol 311 Virial solvent 1.09912E+04 1.72989E+03 1.13858E+03 1.09912E+04 1.72989E+03 1.13858E+03 kJ/mol 312 Energy solvent kinetic uncorrected 2.77071E+04 2.85979E+02 3.59942E+02 2.77071E+04 2.85979E+02 3.59942E+02 kJ/mol 313 Energy solute kinetic uncorrected 4.45653E+03 1.29177E+02 3.44728E+02 4.45653E+03 1.29177E+02 3.44728E+02 kJ/mol 314 Energy kinetic uncorrected 3.21636E+04 3.56410E+02 7.04670E+02 3.21636E+04 3.56410E+02 7.04670E+02 kJ/mol 315 Mean square displacement solvent /6 3.33463E-03 2.00048E-03 6.92868E-03 3.33463E-03 2.00048E-03 6.92868E-03 nm**2 316 Diffusion constant solvent 6.22055E-09 1.19837E-09 2.65492E-09 6.22055E-09 1.19837E-09 2.65492E-09 m**2/s 317 Dipole moment solvent 7.83722E+00 1.72996E-07 4.75194E-08 7.83722E+00 1.72996E-07 4.75194E-08 e30 C m 318 Energy solute 1 intra-Coulombic -1.14329E+04 2.09371E+02 -7.75100E+01 -1.14329E+04 2.09371E+02 -7.75100E+01 kJ/mol 319 Energy solute 1 intra-Lennard-Jones -5.59196E+03 9.63152E+01 1.79973E+02 -5.59196E+03 9.63152E+01 1.79973E+02 kJ/mol 320 Energy solute 1-solvent Coulombic -1.85154E+04 2.29509E+02 -1.52123E+01 -1.85154E+04 2.29509E+02 -1.52123E+01 kJ/mol 321 Energy solute 1-solvent Lennard-Jones-9.37340E+02 1.23019E+02 -8.80722E+01 -9.37340E+02 1.23019E+02 -8.80722E+01 kJ/mol 322 Energy solute 1 bonds 9.46581E+02 5.24592E+01 1.24570E+02 9.46581E+02 5.24592E+01 1.24570E+02 kJ/mol 323 Energy solute 1 angles 2.63918E+03 8.32018E+01 1.62590E+02 2.63918E+03 8.32018E+01 1.62590E+02 kJ/mol 324 Energy solute 1 proper dihedrals 1.05283E+03 4.06988E+01 -3.65332E+01 1.05283E+03 4.06988E+01 -3.65332E+01 kJ/mol 325 Energy solute 1 improper dihedrals 7.22374E+02 3.15617E+01 1.14614E+01 7.22374E+02 3.15617E+01 1.14614E+01 kJ/mol 326 Energy solute 1 Coulombic -1.14329E+04 2.09371E+02 -7.75100E+01 -1.14329E+04 2.09371E+02 -7.75100E+01 kJ/mol 327 Energy solute 1 Lennard-Jones -5.59196E+03 9.63152E+01 1.79973E+02 -5.59196E+03 9.63152E+01 1.79973E+02 kJ/mol 328 Energy solute 1 kinetic translations 4.15313E+00 7.42119E-01 -1.29813E+00 4.15313E+00 7.42119E-01 -1.29813E+00 kJ/mol 329 Energy solute 1 kinetic 4.45622E+03 1.29382E+02 3.45744E+02 4.45622E+03 1.29382E+02 3.45744E+02 kJ/mol 330 Energy solute 1 potential -2.13902E+04 2.49080E+02 3.12908E+02 -2.13902E+04 2.49080E+02 3.12908E+02 kJ/mol 331 Energy solute 1 total -1.69340E+04 3.10303E+02 6.58652E+02 -1.69340E+04 3.10303E+02 6.58652E+02 kJ/mol 332 Virial solute 1 4.69736E+03 1.59143E+03 5.95648E+02 4.69736E+03 1.59143E+03 5.95648E+02 kJ/mol 333 Mean square displacement solute 1 /6 1.25473E-05 6.28617E-06 1.98182E-05 1.25473E-05 6.28617E-06 1.98182E-05 nm**2 334 Diffusion coefficient solute 1 2.47463E-11 7.29231E-12 1.94106E-12 2.47463E-11 7.29231E-12 1.94106E-12 m**2/s 335 336 337 TIMING ANALYSIS 97/06/25 14:50:35 338 339 340 341 342 Timing analysis for node 0 343 344 Number Total CPUtime Percent Percent 345 of CPUtime per process total 346 calls call CPUtime CPUtime 347 348 total 1 496.110 .496 100.827 100.000 349 arg_setup (Setup phase) 1 4.070 .004 .827 .820 350 arg_setlfn (Logical file assignment) 1 .010 .000 .002 .002 351 arg_nrnode (Node distribution) 1 .000 .000 .000 .000 352 memor1 1 1.170 .001 .238 .236 353 setup1 1 2.860 .003 .581 .576 354 memor2 1 .010 .000 .002 .002 355 setup2 1 .020 .000 .004 .004 356 param1 (Parameters pass 1) 1 .050 .000 .010 .010 357 param2 (Parameters pass 2) 1 .010 .000 .002 .002 358 param3 (Parameters pass 3) 1 .030 .000 .006 .006 359 arg_task (Task phase) 1 492.040 .492 100.000 99.180 360 newton (Newtonian time step) 1000 491.980 .492 99.988 99.168 361 init (Time step initialization) 1000 2.620 .003 .532 .528 362 travel (Redistribution) 1001 2.000 .002 .406 .403 363 forces (Forces) 1000 435.160 .435 88.440 87.714 364 forcec (pair potential forces) 1000 435.110 .435 88.430 87.704 365 shakew (SHAKE solvent) 1000 1.940 .002 .394 .391 366 shakes (SHAKE solute) 1000 .000 .000 .000 .000 367 cenmas (Center of mass) 1002 7.590 .008 1.543 1.530 368 fold (Periodic boundaries) 1000 3.640 .004 .740 .734 369 proper (Property calculation) 1000 13.910 .014 2.827 2.804 370 collct (Property collection) 1000 3.940 .004 .801 .794 371 372 Number Total Wall time Percent Percent 373 of Wall time per process total 374 calls call Wall time Wall time 375 376 total 1 497.700 .498 100.931 100.000 377 arg_setup (Setup phase) 1 4.592 .005 .931 .923 378 arg_setlfn (Logical file assignment) 1 .026 .000 .005 .005 379 arg_nrnode (Node distribution) 1 .070 .000 .014 .014 380 memor1 1 1.253 .001 .254 .252 381 setup1 1 2.892 .003 .586 .581 382 memor2 1 .004 .000 .001 .001 383 setup2 1 .271 .000 .055 .054 384 param1 (Parameters pass 1) 1 .049 .000 .010 .010 385 param2 (Parameters pass 2) 1 .017 .000 .003 .003 386 param3 (Parameters pass 3) 1 .027 .000 .005 .005 387 arg_task (Task phase) 1 493.108 .493 100.000 99.077 388 newton (Newtonian time step) 1000 493.038 .493 99.986 99.063 389 init (Time step initialization) 1000 2.537 .003 .514 .510 390 travel (Redistribution) 1001 2.320 .002 .470 .466 391 forces (Forces) 1000 436.264 .436 88.472 87.656 392 forcec (pair potential forces) 1000 436.138 .436 88.639 87.631 393 shakew (SHAKE solvent) 1000 2.104 .002 .427 .423 394 shakes (SHAKE solute) 1000 .032 .000 .006 .006 395 cenmas (Center of mass) 1002 7.601 .008 1.541 1.527 396 fold (Periodic boundaries) 1000 3.569 .004 .724 .717 397 proper (Property calculation) 1000 14.124 .014 2.864 2.838 398 collct (Property collection) 1000 3.811 .004 .773 .766 399 400 401 Number Total Comtime Percent Percent 402 of Comtime per process total 403 calls call Comtime Comtime 404 405 forces 1000 46.781 .047 9.487 9.399 406 407 408 Number Total Syntime Percent Percent 409 of Syntime per process total 410 calls call Syntime Syntime 411 412 travel 1002 1.795 .002 .364 .361 413 forces 1000 36.348 .036 7.371 7.303 414 415 416 Setup Process Per step Total 417 418 Wall clock time in seconds 4.591660 493.108 .493108 497.700 419 CPU time in seconds 4.070000 492.040 .492040 496.110 420 421 422 Global timing analysis 423 424 425 426 Communication time minimum per step .016282 s 427 Communication time maximum per step .054082 s 428 Communication time average per step .044072 s accumulated 2.379894 s 429 430 431 Synchronization time minimum per step .019196 s 432 Synchronization time maximum per step .038413 s 433 Synchronization time average per step .031288 s accumulated 1.689528 s 434 435 436 Wall clock time per MD step .493269 s accumulated 26.636501 s 437 CPU time per MD step .492110 s accumulated 26.573940 s 438 439 440 MEMORY USAGE ANALYSIS 97/06/25 14:50:35 441 442 443 Number of allocated words of memory 7372864 444 Number of unused words of memory 6828447 445 Maximum length solvent-solvent pairlist 746879 446 Maximum length solvent-solute pairlist 280030 447 Maximum length solute-solute pairlist 416350 448 449 450 This run ended on 97/06/25 at 14:50:35 with 0 informative messages 451 and 0 warning messages 452 453 454 DAYFILE 97/06/25 14:50:35 455 456 Date Time Elapsed CPU Routine Dayfile message 457 458 97/06/25 14:42:17 .170 .010 nwARGOS Revision 1.000, prepared 21-sep-95 at 11:48:54 459 97/06/25 14:42:17 .170 .010 start : File day opened formatted 460 97/06/25 14:42:17 .184 .020 rddim : file rst opened formatted 461 97/06/25 14:42:18 .862 .700 rddim : file rst closed 462 97/06/25 14:42:18 .862 .700 rddim : file top opened formatted 463 97/06/25 14:42:18 .987 .830 rddim : file top closed 464 97/06/25 14:42:19 1.364 1.120 memor1 : 8 bytes per word 465 97/06/25 14:42:19 1.364 1.120 memor1 : 2 integer(s) per word 466 97/06/25 14:42:19 1.365 1.120 memor1 : 25650 words for 3128 solvent molecules 467 97/06/25 14:42:19 1.365 1.130 memor1 : 76788 words for 1530 solute atoms 468 97/06/25 14:42:19 1.377 1.140 memor1 : 0 kb for global array ip 469 97/06/25 14:42:19 1.384 1.140 memor1 : 9 kb for global array iw 470 97/06/25 14:42:19 1.391 1.150 memor1 : 189 kb for global array w 471 97/06/25 14:42:19 1.397 1.160 memor1 : 77 kb for global array is 472 97/06/25 14:42:19 1.404 1.160 memor1 : 466 kb for global array s 473 97/06/25 14:42:19 1.404 1.160 memor1 : 741 kb total for global arrays 474 97/06/25 14:42:19 1.423 1.180 memor1 : 766108 words of ga-memory allocated in ma-space 475 97/06/25 14:42:19 1.424 1.180 malloc : 7372864 words of memory allocated 476 97/06/25 14:42:19 1.427 1.190 memor2 : 140911 words of memory used for workarrays 477 97/06/25 14:42:19 1.428 1.190 memor2 : 305205 words of memory assigned 478 97/06/25 14:42:19 1.428 1.190 memor2 : 6926748 words of memory available 479 97/06/25 14:42:19 1.430 1.190 rdstrt : File rst opened formatted 480 97/06/25 14:42:20 2.752 2.510 rdstrt : File rst closed 481 97/06/25 14:42:20 2.752 2.510 rdtop : File top opened formatted 482 97/06/25 14:42:21 3.674 3.430 rdtop : File top closed 483 97/06/25 14:42:21 3.772 3.530 param1 : Parameter calculations pass 1 484 97/06/25 14:42:21 3.773 3.530 param1 : emsl FFT routine 485 97/06/25 14:42:21 3.773 3.530 param1 : FFT integer worklength 208 486 97/06/25 14:42:21 3.773 3.530 param1 : FFT real worklength 65610 487 97/06/25 14:42:21 3.820 3.580 param1 : Reaction field setup completed 488 97/06/25 14:42:21 3.821 3.580 param1 : Mass factors calculation completed 489 97/06/25 14:42:21 3.821 3.580 param1 : Parameter calculations pass 1 completed 490 97/06/25 14:42:21 4.047 3.810 param2 : Parameter calculations pass 2 491 97/06/25 14:42:21 4.061 3.820 param2 : Parameter calculations pass 2 completed 492 97/06/25 14:42:21 4.065 3.830 param3 : Parameter calculations pass 3 493 97/06/25 14:42:21 4.072 3.830 param3 : Index array solute third neighbor list generated 494 97/06/25 14:42:21 4.073 3.830 param3 : Index array solute excluded pairlist generated 495 97/06/25 14:42:21 4.088 3.850 param3 : Parameter calculations pass 3 completed 496 97/06/25 14:42:21 4.090 3.850 param4 : Parameter calculations pass 4 497 97/06/25 14:42:21 4.090 3.850 param4 : Parameter calculations pass 4 completed 498 97/06/25 14:42:21 4.090 3.850 param5 : Parameter calculations pass 5 499 97/06/25 14:42:21 4.090 3.850 param5 : Parameter calculations pass 5 completed 500 97/06/25 14:42:21 4.116 3.850 openf2 : File out opened formatted 501 97/06/25 14:42:21 4.124 3.850 openf2 : File tst opened formatted 502 97/06/25 14:42:21 4.124 3.850 openf2 : File initialization completed 503 97/06/25 14:42:22 4.590 4.070 wrtinp : Completed 504 97/06/25 14:42:22 4.592 4.070 task : calculation driver routine 505 97/06/25 14:42:22 4.635 4.120 dynam : Single run molecular dynamics simulation 506 97/06/25 14:50:35 497.699 496.110 dynam : Single run molecular dynamics simulation completed 507 97/06/25 14:50:35 497.700 496.110 task : Calculation completed 508 97/06/25 14:50:35 497.700 496.110 closef : File syn closed 509 97/06/25 14:50:35 497.770 496.180 finish : Completed with 0 informative messages 510 97/06/25 14:50:35 497.770 496.180 finish : Completed with 0 warning messages 511