Dear All
I'm trying to perform a Car-Parrinello calculation on a box of benzene molecules. I'm using pspw for structural optimization of the moeclues before running MD simulation. However, when I look at the optimized structure of the simulation box, it seems that all of the benzene molecules have been broken and their C and H atoms have been separated. Please guide we how can I solve this problem. I appreciate you help. My input file is as follows:
title "benzene ab initio MD"
memory 1000 mb
start benzene20.nw
geometry units angstroms
C -2.84313711 0.40305010 0.00000000
C -1.44797711 0.40305010 0.00000000
C -0.75043911 1.61080110 0.00000000
C -1.44809311 2.81931010 -0.00119900
C -2.84291811 2.81923210 -0.00167800
C -3.54051911 1.61102610 -0.00068200
H -3.39289611 -0.54926690 0.00045000
H -0.89846911 -0.54946290 0.00131500
H 0.34924089 1.61088110 0.00063400
H -0.89789311 3.77145310 -0.00125800
H -3.39304011 3.77151310 -0.00263100
H -4.64012311 1.61120910 -0.00086200
C 6.56721800 3.10590793 -0.00056443
C 7.96237800 3.10590793 -0.00056443
C 8.65991600 4.31365893 -0.00056443
C 7.96226200 5.52216793 -0.00176343
C 6.56743700 5.52208993 -0.00224243
C 5.86983600 4.31388393 -0.00124643
H 6.01745900 2.15359093 -0.00011443
H 8.51188600 2.15339493 0.00075057
H 9.75959600 4.31373893 0.00006957
H 8.51246200 6.47431093 -0.00182243
H 6.01731500 6.47437093 -0.00319543
H 4.77023200 4.31406693 -0.00142643
C 3.29114260 -3.91373234 -1.23235702
C 4.68630260 -3.91373234 -1.23235702
C 5.38384060 -2.70598134 -1.23235702
C 4.68618660 -1.49747234 -1.23355602
C 3.29136160 -1.49755034 -1.23403502
C 2.59376060 -2.70575634 -1.23303902
H 2.74138360 -4.86604934 -1.23190702
H 5.23581060 -4.86624534 -1.23104202
H 6.48352060 -2.70590134 -1.23172302
H 5.23638660 -0.54532934 -1.23361502
H 2.74123960 -0.54526934 -1.23498802
H 1.49415660 -2.70557334 -1.23321902
C 3.46434244 2.54568378 -4.50747046
C 4.85950244 2.54568378 -4.50747046
C 5.55704044 3.75343478 -4.50747046
C 4.85938644 4.96194378 -4.50866946
C 3.46456144 4.96186578 -4.50914846
C 2.76696044 3.75365978 -4.50815246
H 2.91458344 1.59336678 -4.50702046
H 5.40901044 1.59317078 -4.50615546
H 6.65672044 3.75351478 -4.50683646
H 5.40958644 5.91408678 -4.50872846
H 2.91443944 5.91414678 -4.51010146
H 1.66735644 3.75384278 -4.50833246
C 2.00829885 -4.26356223 -6.23781143
C 3.40345885 -4.26356223 -6.23781143
C 4.10099685 -3.05581123 -6.23781143
C 3.40334285 -1.84730223 -6.23901043
C 2.00851785 -1.84738023 -6.23948943
C 1.31091685 -3.05558623 -6.23849343
H 1.45853985 -5.21587923 -6.23736143
H 3.95296685 -5.21607523 -6.23649643
H 5.20067685 -3.05573123 -6.23717743
H 3.95354285 -0.89515923 -6.23906943
H 1.45839585 -0.89509923 -6.24044243
H 0.21131285 -3.05540323 -6.23867343
C 3.33541761 4.98815425 4.81666324
C 4.73057761 4.98815425 4.81666324
C 5.42811561 6.19590525 4.81666324
C 4.73046161 7.40441425 4.81546424
C 3.33563661 7.40433625 4.81498524
C 2.63803561 6.19613025 4.81598124
H 2.78565861 4.03583725 4.81711324
H 5.28008561 4.03564125 4.81797824
H 6.52779561 6.19598525 4.81729724
H 5.28066161 8.35655725 4.81540524
H 2.78551461 8.35661725 4.81403224
H 1.53843161 6.19631325 4.81580124
C -0.24724487 -1.47647025 5.70034460
C 1.14791513 -1.47647025 5.70034460
C 1.84545313 -0.26871925 5.70034460
C 1.14779913 0.93978975 5.69914560
C -0.24702587 0.93971175 5.69866660
C -0.94462687 -0.26849425 5.69966260
H -0.79700387 -2.42878725 5.70079460
H 1.69742313 -2.42898325 5.70165960
H 2.94513313 -0.26863925 5.70097860
H 1.69799913 1.89193275 5.69908660
H -0.79714787 1.89199275 5.69771360
H -2.04423087 -0.26831125 5.69948260
C 5.22117859 11.16506489 1.52523606
C 6.61633859 11.16506489 1.52523606
C 7.31387659 12.37281589 1.52523606
C 6.61622259 13.58132489 1.52403706
C 5.22139759 13.58124689 1.52355806
C 4.52379659 12.37304089 1.52455406
H 4.67141959 10.21274789 1.52568606
H 7.16584659 10.21255189 1.52655106
H 8.41355659 12.37289589 1.52587006
H 7.16642259 14.53346789 1.52397806
H 4.67127559 14.53352789 1.52260506
H 3.42419259 12.37322389 1.52437406
C 6.28114930 10.83182567 -4.09687482
C 7.67630930 10.83182567 -4.09687482
C 8.37384730 12.03957667 -4.09687482
C 7.67619330 13.24808567 -4.09807382
C 6.28136830 13.24800767 -4.09855282
C 5.58376730 12.03980167 -4.09755682
H 5.73139030 9.87950867 -4.09642482
H 8.22581730 9.87931267 -4.09555982
H 9.47352730 12.03965667 -4.09624082
H 8.22639330 14.20022867 -4.09813282
H 5.73124630 14.20028867 -4.09950582
H 4.48416330 12.03998467 -4.09773682
C 0.74015125 -9.53571503 -3.88960054
C 2.13531125 -9.53571503 -3.88960054
C 2.83284925 -8.32796403 -3.88960054
C 2.13519525 -7.11945503 -3.89079954
C 0.74037025 -7.11953303 -3.89127854
C 0.04276925 -8.32773903 -3.89028254
H 0.19039225 -10.48803203 -3.88915054
H 2.68481925 -10.48822803 -3.88828554
H 3.93252925 -8.32788403 -3.88896654
H 2.68539525 -6.16731203 -3.89085854
H 0.19024825 -6.16725203 -3.89223154
H -1.05683475 -8.32755603 -3.89046254
C -0.48263307 -9.04142894 3.33293378
C 0.91252693 -9.04142894 3.33293378
C 1.61006493 -7.83367794 3.33293378
C 0.91241093 -6.62516894 3.33173478
C -0.48241407 -6.62524694 3.33125578
C -1.18001507 -7.83345294 3.33225178
H -1.03239207 -9.99374594 3.33338378
H 1.46203493 -9.99394194 3.33424878
H 2.70974493 -7.83359794 3.33356778
H 1.46261093 -5.67302594 3.33167578
H -1.03253607 -5.67296594 3.33030278
H -2.27961907 -7.83326994 3.33207178
C 3.60206643 9.87984273 9.01740630
C 4.99722643 9.87984273 9.01740630
C 5.69476443 11.08759373 9.01740630
C 4.99711043 12.29610273 9.01620730
C 3.60228543 12.29602473 9.01572830
C 2.90468443 11.08781873 9.01672430
H 3.05230743 8.92752573 9.01785630
H 5.54673443 8.92732973 9.01872130
H 6.79444443 11.08767373 9.01804030
H 5.54731043 13.24824573 9.01614830
H 3.05216343 13.24830573 9.01477530
H 1.80508043 11.08800173 9.01654430
C -0.59901864 -5.56448244 9.16997053
C 0.79614136 -5.56448244 9.16997053
C 1.49367936 -4.35673144 9.16997053
C 0.79602536 -3.14822244 9.16877153
C -0.59879964 -3.14830044 9.16829253
C -1.29640064 -4.35650644 9.16928853
H -1.14877764 -6.51679944 9.17042053
H 1.34564936 -6.51699544 9.17128553
H 2.59335936 -4.35665144 9.17060453
H 1.34622536 -2.19607944 9.16871253
H -1.14892164 -2.19601944 9.16733953
H -2.39600464 -4.35632344 9.16910853
C 1.33400275 3.34912227 11.86760801
C 2.72916275 3.34912227 11.86760801
C 3.42670075 4.55687327 11.86760801
C 2.72904675 5.76538227 11.86640901
C 1.33422175 5.76530427 11.86593001
C 0.63662075 4.55709827 11.86692601
H 0.78424375 2.39680527 11.86805801
H 3.27867075 2.39660927 11.86892301
H 4.52638075 4.55695327 11.86824201
H 3.27924675 6.71752527 11.86635001
H 0.78409975 6.71758527 11.86497701
H -0.46298325 4.55728127 11.86674601
C 5.50138545 3.67436488 -9.12684400
C 6.89654545 3.67436488 -9.12684400
C 7.59408345 4.88211588 -9.12684400
C 6.89642945 6.09062488 -9.12804300
C 5.50160445 6.09054688 -9.12852200
C 4.80400345 4.88234088 -9.12752600
H 4.95162645 2.72204788 -9.12639400
H 7.44605345 2.72185188 -9.12552900
H 8.69376345 4.88219588 -9.12621000
H 7.44662945 7.04276788 -9.12810200
H 4.95148245 7.04282788 -9.12947500
H 3.70439945 4.88252388 -9.12770600
C 11.02132949 -2.54403824 2.71465663
C 12.41648949 -2.54403824 2.71465663
C 13.11402749 -1.33628724 2.71465663
C 12.41637349 -0.12777824 2.71345763
C 11.02154849 -0.12785624 2.71297863
C 10.32394749 -1.33606224 2.71397463
H 10.47157049 -3.49635524 2.71510663
H 12.96599749 -3.49655124 2.71597163
H 14.21370749 -1.33620724 2.71529063
H 12.96657349 0.82436476 2.71339863
H 10.47142649 0.82442476 2.71202563
H 9.22434349 -1.33587924 2.71379463
C 13.78920316 6.75755241 2.24113162
C 15.18436316 6.75755241 2.24113162
C 15.88190116 7.96530341 2.24113162
C 15.18424716 9.17381241 2.23993262
C 13.78942216 9.17373441 2.23945362
C 13.09182116 7.96552841 2.24044962
H 13.23944416 5.80523541 2.24158162
H 15.73387116 5.80503941 2.24244662
H 16.98158116 7.96538341 2.24176562
H 15.73444716 10.12595541 2.23987362
H 13.23930016 10.12601541 2.23850062
H 11.99221716 7.96571141 2.24026962
C -3.16492565 9.73512139 0.64628811
C -1.76976565 9.73512139 0.64628811
C -1.07222765 10.94287239 0.64628811
C -1.76988165 12.15138139 0.64508911
C -3.16470665 12.15130339 0.64461011
C -3.86230765 10.94309739 0.64560611
H -3.71468465 8.78280439 0.64673811
H -1.22025765 8.78260839 0.64760311
H 0.02745235 10.94295239 0.64692211
H -1.21968165 13.10352439 0.64503011
H -3.71482865 13.10358439 0.64365711
H -4.96191165 10.94328039 0.64542611
C -9.81118236 -5.77029034 1.89259097
C -8.41602236 -5.77029034 1.89259097
C -7.71848436 -4.56253934 1.89259097
C -8.41613836 -3.35403034 1.89139197
C -9.81096336 -3.35410834 1.89091297
C -10.50856436 -4.56231434 1.89190897
H -10.36094136 -6.72260734 1.89304097
H -7.86651436 -6.72280334 1.89390597
H -6.61880436 -4.56245934 1.89322497
H -7.86593836 -2.40188734 1.89133297
H -10.36108536 -2.40182734 1.88995997
H -11.60816836 -4.56213134 1.89172897
C 9.90336105 -10.28465062 3.00244024
C 11.29852105 -10.28465062 3.00244024
C 11.99605905 -9.07689962 3.00244024
C 11.29840505 -7.86839062 3.00124124
C 9.90358005 -7.86846862 3.00076224
C 9.20597905 -9.07667462 3.00175824
H 9.35360205 -11.23696762 3.00289024
H 11.84802905 -11.23716362 3.00375524
H 13.09573905 -9.07681962 3.00307424
H 11.84860505 -6.91624762 3.00118224
H 9.35345805 -6.91618762 2.99980924
H 8.10637505 -9.07649162 3.00157824
C -9.47455691 3.14429790 0.17000194
C -8.07939691 3.14429790 0.17000194
C -7.38185891 4.35204890 0.17000194
C -8.07951291 5.56055790 0.16880294
C -9.47433791 5.56047990 0.16832394
C -10.17193891 4.35227390 0.16931994
H -10.02431591 2.19198090 0.17045194
H -7.52988891 2.19178490 0.17131694
H -6.28217891 4.35212890 0.17063594
H -7.52931291 6.51270090 0.16874394
H -10.02445991 6.51276090 0.16737094
H -11.27154291 4.35245690 0.16913994
end
charge 0
nwpw
xc pbe96
cutoff 50.0
end
pspw
simulation_cell units angstroms
boundary_conditions periodic
lattice
lat_a 17.00d0
lat_b 17.00d0
lat_c 17.00d0
end
ngrid 30 30 30
end
Car-Parrinello
Nose-Hoover 1200.0 300.0
fake_mass 600.0
time_step 1.0
loop 100 100
end
end
set nwpw:minimizer 2
task pspw optimize
task pspw Car-Parrinello
|