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 ENERGY MINIMIZATION 18 19 Title input NWChem:nwARGOS input Creation date 97/07/28 20 Creation time 12:50:51 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 97/07/28 29 Today's time 12:50:51 30 31 32 33 34 FORCE FIELD gromos 35 36 37 38 39 40 ATOMIC DATA 97/07/28 12:50:59 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 97/07/28 12:50:59 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 0.001000 104 solute 0.001000 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 0.900000 0.900000 110 solute -solvent 0.900000 0.900000 0.900000 0.900000 111 solute -solute 0.900000 0.900000 0.900000 0.900000 0.900000 0.900000 112 qmmm boundary 0.900000 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 ENERGY MINIMIZATION PARAMETERS 97/07/28 12:50:59 128 129 130 Number of minimizations 0 Frequency solvent-solvent pairlist 1 131 Frequency coordinate read 0 Frequency solvent-solute pairlist 1 132 Frequency QRS update 25 133 Energy criterion 3 Parameter set number 1 134 135 Minimization algorithm Steepest descent Conjugate gradient 136 137 Maximum number of minimization steps 5 5 138 Frequency starting fresh cycle 10 139 140 Step size threshold 0.000010 0.000010 nm 141 Initial step length 0.010000 0.010000 nm 142 Maximum step length 0.050000 nm 143 144 145 DIMENSIONS AT INITIALIZATION 97/07/28 12:50:59 146 147 MAT : max number of atom types 24 MAXW : max length of work arrays 3844 148 MWM : max number of solvent molecules 3844 MSM : max number of solute molecules 5 149 MWA : max number of solvent atoms 3 MSA : max number of solute atoms 3061 150 MWB : max number of solvent bonds 3 MSB : max number of solute bonds 1566 151 MWH : max number of solvent angles 1 MSH : max number of solute angles 2269 152 MWD : max number of solvent proper dihedrals 1 MSD : max number of solute proper dihedrals 1664 153 MWO : max number of solvent improper dihedrals 1 MSO : max number of solute improper dihedrals 777 154 MSG : max number of solute groups 948 155 MSS : max number of solute segments 154 156 MPN : max length of property arrays 172 157 MGC : max number RDF contributions 1 SMALL : small real number 1.00E-12 158 MGR : max number RDF's 1 TINY : tiny real number 1.00E-14 159 MGL : max length RDF's 1 SIL : sin(dihedral) algorithm change 0.001000 160 MSHITW: max number solvent SHAKE iterations 100 MSHITS: max number solute SHAKE iterations 100 161 162 163 SPACIAL DECOMPOSITION INFORMATION 97/07/28 12:50:59 164 165 166 Largest number of sub-boxes in one dimension 5 167 Largest number of sub-boxes per node 125 168 169 Number of additional sub-boxes per node 6 170 171 No load balancing 172 173 Number of nodes 1 divided 1 x 1 x 1 174 Number of boxes 125 divided 5 x 5 x 5 175 176 Initial distribution of box-box pairs 177 178 Node Pairs 179 0 1750 180 181 Initial number of solvent molecules 182 183 Node nwm 184 0 3128 185 186 Initial number of solute atoms 187 188 Node nsa 189 0 1530 190 191 ENERGY MINIMIZATION STEP INFORMATION 97/07/28 12:50:59 192 193 irec sdit cgit cgcy esddiff ecgdiff ediftot ess esw eww epot dxmax 194 1 1 -0.38973E+02 0.00000E+00 -0.38973E+02 -0.10410E+05 -0.19322E+05 -0.10996E+06 -0.13969E+06 0.00006976 195 2 2 -0.47384E+02 0.00000E+00 -0.86357E+02 -0.10422E+05 -0.19325E+05 -0.10999E+06 -0.13974E+06 0.00008312 196 3 3 -0.55900E+02 0.00000E+00 -0.14226E+03 -0.10435E+05 -0.19328E+05 -0.11003E+06 -0.13979E+06 0.00009890 197 4 4 -0.66499E+02 0.00000E+00 -0.20876E+03 -0.10451E+05 -0.19331E+05 -0.11008E+06 -0.13986E+06 0.00011748 198 5 * 5 -0.79554E+02 0.00000E+00 -0.28831E+03 -0.10470E+05 -0.19335E+05 -0.11013E+06 -0.13994E+06 0.00013927 199 6 1 1 0.00000E+00 -0.27903E+02 -0.27903E+02 -0.10476E+05 -0.19337E+05 -0.11015E+06 -0.13997E+06 0.00004065 200 7 2 1 0.00000E+00 -0.33111E+02 -0.61014E+02 -0.10483E+05 -0.19343E+05 -0.11017E+06 -0.14000E+06 0.00004075 201 8 3 1 0.00000E+00 -0.27195E+02 -0.88208E+02 -0.10489E+05 -0.19345E+05 -0.11019E+06 -0.14003E+06 0.00003974 202 9 * 4 1 0.00000E+00 -0.26967E+02 -0.11518E+03 -0.10496E+05 -0.19346E+05 -0.11021E+06 -0.14005E+06 0.00003975 203 10 * 5 1 0.00000E+00 -0.27131E+02 -0.14231E+03 -0.10502E+05 -0.19348E+05 -0.11023E+06 -0.14008E+06 0.00003984 204 205 206 TIMING ANALYSIS 97/07/28 12:54:05 207 208 209 210 211 Timing analysis for node 0 212 213 Number Total CPUtime Percent Percent 214 of CPUtime per process total 215 calls call CPUtime CPUtime 216 217 total 1 185.519 18.552 104.013 100.000 218 arg_setup (Setup phase) 1 7.158 0.716 4.013 3.858 219 arg_setlfn (Logical file assignment) 1 0.001 0.000 0.001 0.001 220 arg_nrnode (Node distribution) 1 0.000 0.000 0.000 0.000 221 memor1 1 1.899 0.190 1.065 1.024 222 setup1 1 4.277 0.428 2.398 2.306 223 memor2 1 0.025 0.003 0.014 0.014 224 setup2 1 0.952 0.095 0.534 0.513 225 param1 (Parameters pass 1) 1 0.028 0.003 0.016 0.015 226 param2 (Parameters pass 2) 1 0.000 0.000 0.000 0.000 227 param3 (Parameters pass 3) 1 0.039 0.004 0.022 0.021 228 arg_task (Task phase) 1 178.360 17.836 100.000 96.141 229 init (Time step initialization) 21 0.429 0.043 0.240 0.231 230 travel (Redistribution) 1 0.263 0.026 0.147 0.142 231 forces (Forces) 21 170.430 17.043 95.553 91.866 232 forcec (pair potential forces) 21 170.409 17.041 95.542 91.855 233 shakew (SHAKE solvent) 21 1.328 0.133 0.745 0.716 234 shakes (SHAKE solute) 21 0.060 0.006 0.034 0.032 235 cenmas (Center of mass) 2 0.010 0.001 0.006 0.005 236 proper (Property calculation) 21 0.639 0.064 0.358 0.345 237 collct (Property collection) 21 0.007 0.001 0.004 0.004 238 239 Number Total Wall time Percent Percent 240 of Wall time per process total 241 calls call Wall time Wall time 242 243 total 1 194.197 19.420 104.103 100.000 244 arg_setup (Setup phase) 1 7.654 0.765 4.103 3.941 245 arg_setlfn (Logical file assignment) 1 0.001 0.000 0.001 0.001 246 arg_nrnode (Node distribution) 1 0.000 0.000 0.000 0.000 247 memor1 1 1.994 0.199 1.069 1.027 248 setup1 1 4.582 0.458 2.456 2.359 249 memor2 1 0.027 0.003 0.015 0.014 250 setup2 1 1.029 0.103 0.551 0.530 251 param1 (Parameters pass 1) 1 0.030 0.003 0.016 0.015 252 param2 (Parameters pass 2) 1 0.000 0.000 0.000 0.000 253 param3 (Parameters pass 3) 1 0.040 0.004 0.022 0.021 254 arg_task (Task phase) 1 186.543 18.654 100.000 96.059 255 init (Time step initialization) 21 0.462 0.046 0.247 0.238 256 travel (Redistribution) 1 0.261 0.026 0.140 0.134 257 forces (Forces) 21 178.371 17.837 95.620 91.851 258 forcec (pair potential forces) 21 178.349 17.835 99.994 91.840 259 shakew (SHAKE solvent) 21 1.344 0.134 0.720 0.692 260 shakes (SHAKE solute) 21 0.061 0.006 0.033 0.032 261 cenmas (Center of mass) 2 0.012 0.001 0.006 0.006 262 proper (Property calculation) 21 0.674 0.067 0.361 0.347 263 collct (Property collection) 21 0.007 0.001 0.004 0.004 264 265 266 Number Total Comtime Percent Percent 267 of Comtime per process total 268 calls call Comtime Comtime 269 270 forces 21 1.124 0.112 0.602 0.579 271 272 273 Number Total Syntime Percent Percent 274 of Syntime per process total 275 calls call Syntime Syntime 276 277 travel 2 0.000 0.000 0.000 0.000 278 forces 21 0.003 0.000 0.001 0.001 279 280 281 Setup Process Per step Total 282 283 Wall clock time in seconds 7.653896 186.543 18.654262 194.197 284 CPU time in seconds 7.158297 178.360 17.836048 185.519 285 286 287 Global timing analysis 288 289 290 291 Communication time minimum per step 0.112389 s 292 Communication time maximum per step 0.112389 s 293 Communication time average per step 0.112389 s accumulated 0.112389 s 294 295 296 Synchronization time minimum per step 0.000276 s 297 Synchronization time maximum per step 0.000276 s 298 Synchronization time average per step 0.000276 s accumulated 0.000276 s 299 300 301 Wall clock time per EM step 18.654262 s accumulated 18.654262 s 302 CPU time per EM step 17.836048 s accumulated 17.836048 s 303 304 305 MEMORY USAGE ANALYSIS 97/07/28 12:54:05 306 307 308 Number of allocated words of memory 2881108 309 Number of unused words of memory 1098394 310 Maximum length solvent-solvent pairlist 137928 311 Maximum length solvent-solute pairlist 32419 312 Maximum length solute-solute pairlist 102678 313 314 315 This run ended on 97/07/28 at 12:54:05 with 0 informative messages 316 and 0 warning messages 317 318 319 DAYFILE 97/07/28 12:54:05 320 321 Date Time Elapsed CPU Routine Dayfile message 322 323 97/07/28 12:50:51 0.021 0.004 nwARGOS Revision 1.000, prepared 21-sep-95 at 11:48:54 324 97/07/28 12:50:51 0.022 0.005 start : File day opened formatted 325 97/07/28 12:50:51 0.067 0.047 rddim : file rst opened formatted 326 97/07/28 12:50:53 1.601 1.514 rddim : file rst closed 327 97/07/28 12:50:53 1.602 1.515 rddim : file top opened formatted 328 97/07/28 12:50:53 2.006 1.894 rddim : file top closed 329 97/07/28 12:50:53 2.007 1.895 memor1 : 8 bytes per word 330 97/07/28 12:50:53 2.007 1.895 memor1 : 1 integer(s) per word 331 97/07/28 12:50:53 2.008 1.896 memor1 : 3844 words for 3128 solvent molecules 332 97/07/28 12:50:53 2.008 1.896 memor1 : 3061 words for 1530 solute atoms 333 97/07/28 12:50:53 2.009 1.897 memor1 : 8 kb for global array ip 334 97/07/28 12:50:53 2.010 1.898 memor1 : 150 kb for global array iw 335 97/07/28 12:50:53 2.011 1.899 memor1 : 1531 kb for global array w 336 97/07/28 12:50:53 2.012 1.900 memor1 : 334 kb for global array is 337 97/07/28 12:50:53 2.014 1.902 memor1 : 1004 kb for global array s 338 97/07/28 12:50:53 2.015 1.902 memor1 : 3027 kb total for global arrays 339 97/07/28 12:50:53 2.015 1.903 memor1 : 3106920 words of ga-memory 340 97/07/28 12:50:53 2.016 1.903 memor1 : 5281688 words of ga-memory unused 341 97/07/28 12:50:53 2.017 1.904 malloc : 2881108 words of memory allocated 342 97/07/28 12:50:53 2.042 1.928 memor2 : 207583 words of memory used for workarrays 343 97/07/28 12:50:53 2.042 1.929 memor2 : 945665 words of memory assigned 344 97/07/28 12:50:53 2.044 1.929 memor2 : 1727860 words of memory available 345 97/07/28 12:50:53 2.045 1.931 rdstrt : File rst opened formatted 346 97/07/28 12:50:55 3.737 3.485 rdstrt : File rst closed 347 97/07/28 12:50:55 3.762 3.503 rdtop : File top opened formatted 348 97/07/28 12:50:57 5.774 5.379 rdtop : File top closed 349 97/07/28 12:50:57 5.859 5.460 param1 : Parameter calculations pass 1 350 97/07/28 12:50:57 5.860 5.461 param1 : emsl FFT routine 351 97/07/28 12:50:57 5.860 5.461 param1 : FFT integer worklength 102 352 97/07/28 12:50:57 5.861 5.462 param1 : FFT real worklength 65557 353 97/07/28 12:50:57 5.874 5.474 param1 : Reaction field setup completed 354 97/07/28 12:50:57 5.877 5.477 param1 : Mass factors calculation completed 355 97/07/28 12:50:57 5.888 5.488 param1 : Parameter calculations pass 1 completed 356 97/07/28 12:50:57 6.252 5.837 param3 : Parameter calculations pass 3 357 97/07/28 12:50:57 6.289 5.872 param3 : Index array solute third neighbor list generated 358 97/07/28 12:50:57 6.291 5.874 param3 : Index array solute excluded pairlist generated 359 97/07/28 12:50:57 6.291 5.875 param3 : Parameter calculations pass 3 completed 360 97/07/28 12:50:57 6.292 5.875 param4 : Parameter calculations pass 4 361 97/07/28 12:50:57 6.294 5.877 param4 : Parameter calculations pass 4 completed 362 97/07/28 12:50:57 6.294 5.877 param5 : Parameter calculations pass 5 363 97/07/28 12:50:57 6.295 5.878 param5 : Parameter calculations pass 5 completed 364 97/07/28 12:50:57 6.296 5.879 openf2 : File out opened formatted 365 97/07/28 12:50:57 6.297 5.880 openf2 : File tst opened formatted 366 97/07/28 12:50:57 6.297 5.880 openf2 : File initialization completed 367 97/07/28 12:50:59 7.654 7.158 wrtinp : Completed 368 97/07/28 12:50:59 7.655 7.159 task : calculation driver routine 369 97/07/28 12:50:59 7.666 7.170 minim : energy minimization 370 97/07/28 12:52:27 96.158 91.093 wrstrt : File rst at EM-step 5+ 0 371 97/07/28 12:53:47 175.768 167.481 wrstrt : File rst at EM-step 5+ 4 372 97/07/28 12:54:05 194.196 185.518 wrstrt : File rst at EM-step 5+ 5 373 97/07/28 12:54:05 194.197 185.519 minim : energy minimization completed 374 97/07/28 12:54:05 194.197 185.519 task : Calculation completed 375 97/07/28 12:54:05 194.210 185.532 finish : Completed with 0 informative messages 376 97/07/28 12:54:05 194.211 185.532 finish : Completed with 0 warning messages 377