# dl_poly energy with atomistic cutoff # fragment c unknown persistent c_create coords=c { coordinates angstrom O .6737543037 -2.533871039 4.341299547 H .3135705220 -2.431626305 3.414038166 H .9946264752E-01 -3.172722493 4.853215483 O -5.091042518 1.366291671 -1.167586373 H -5.405973075 .4567850067 -1.438909764 H -4.208816591 1.555693923 -1.598636499 O -5.989740295 -3.708912318 4.930828310 H -6.941738378 -3.545475368 4.672007861 H -5.548910139 -4.278326225 4.236971993 O 4.250102944 -1.629648908 2.597704042 H 4.009262652 -1.745741988 1.634107466 H 3.526715624 -1.119319227 3.062757173 O 4.885182104 -4.163716067 .5431817872 H 5.140618605 -4.496705223 -.3644912949 H 5.000631041 -4.898033102 1.212098854 O 2.441074866 -.2363867131 3.924091009 H 2.012439929 -1.115011131 4.134545845 H 1.735750820 .4270640996 3.674389137 O -3.694941341 6.196234169 1.499957614 H -3.583015051 6.419989528 2.468154936 H -4.391404992 6.791265739 1.098864331 O -6.798001922 -5.879490284 -2.684927117 H -7.168387756 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-1.764366574 -3.619868010 H 5.011375679 -1.853085409 -2.534390400 O 7.236059151 -7.088851159 1.033484832 H 7.346058476 -6.272219015 .4669055376 H -7.269692780 7.183156358 .6348056388 O 4.574687687 -7.383276071 1.163229468 H 4.432860705 7.002179686 1.917309713 H 5.552792439 -7.308443065 .9690359382 O -3.540539718 .2864744847 6.322053387 H -4.408173964 .7285408442 6.094483265 H -2.789078762 .9276485825 6.166482761 O -.9320119628 -5.384160784 -.7588229294 H -1.905163327 -5.231783711 -.5863188384 H -.4166253793 -4.565393204 -.5058479693 O 4.542498698 1.775448143 3.677490573 H 4.916280730 2.095762093 4.547942167 H 3.827089870 1.098634415 3.851022692 O -3.494726466 -.8741508448 -6.205927393 H -3.074706551 -.6879438469 -7.094133583 H -3.836528413 -1.813778705 -6.189467674 O -5.008221487 -5.791655122 3.328201535 H -4.847611801 -5.866641111 2.344036081 H -4.192332190 -6.091329369 3.822691182 O -6.444634157 .9682067665E-01 -5.877772997 H -5.446039324 .9090966733E-01 -5.825109621 H -6.737448190 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1.385389906 H 3.185167236 .1047049461 .8058144924 O -4.838003088 -5.065247807 -4.770199746 H -5.465786720 -5.010075174 -3.993769647 H -4.884718498 -4.216755882 -5.297342167 O 2.834121580 -4.538589323 -1.986850484 H 3.825477575 -4.575004628 -1.860805938 H 2.543298208 -5.302274036 -2.563224873 O .3221354337 .9685600622 -2.586412590 H 1.302879218 1.094855824 -2.437446063 H .1185565555 1.061219547 -3.561076571 O 5.706301757 2.370250056 6.265335650 H 6.271944774 1.566318697 6.081644721 H 6.284728202 3.116195283 6.595469831 O -3.223649041 4.806783954 -3.605395276 H -3.506342524 5.725938140 -3.879694360 H -2.436492028 4.523013634 -4.152988419 O -1.655516165 2.153071608 6.056807027 H -2.201777630 2.781117978 6.611023755 H -.7833391157 1.978095891 6.513633803 O -5.889736461 -2.498927846 2.128485552 H -5.778710947 -2.366930859 3.113498313 H -5.445363831 -1.748254396 1.639586437 O -5.257692279 7.211360039 -1.238692303 H -4.561562468 7.109981488 -1.949414248 H -5.596620285 6.308793444 -.9731713858 O -4.408245394 -5.908664794 .6637752142 H -4.785478775 -6.531594640 -.2153741116E-01 H -3.894754274 -5.182264869 .2069710686 O 2.888799195 -5.340159504 5.150030345 H 2.016630401 -5.649945489 5.528651852 H 2.873532699 -5.437963902 4.154941785 O .2362151269 .7389324341 2.603835032 H -.3939825759 -.2010715105E-01 2.767266278 H -.2619313110 1.604043953 2.662419963 O 7.032489323 -.9897851697 -3.806026530 H -7.395565581 -.6707641750 -4.540736896 H 6.365224574 -.2778420837 -3.587177707 O -4.222410600 6.553015361 4.215778326 H -3.465471417 7.126508610 4.529065053 H -4.811266759 6.325631163 4.991371555 O 1.069925301 -3.642932820 -.2153531032 H .9505089866 -2.659838144 -.7655607287E-01 H 1.768048565 -3.798334624 -.9142623983 O -.4243514956 6.596722856 3.367036453 H .3360834901 6.470500216 4.004065877 H -.6307507281 5.727284790 2.918174765 O -3.883349339 3.654608670 .8173609247 H -3.825673306 4.611832424 1.100903109 H -4.836046167 3.352967187 .8545251531 O -3.459458977 -7.176191133 -3.560785493 H -2.649697298 -6.977233009 -3.008787577 H -3.877197202 -6.318530127 -3.860639432 O -7.199339350 -4.643660458 -.4048820150E-01 H -6.259339755 -4.734376798 .2884058782 H 7.394881681 -3.856833768 .3997723345 O -6.116591494 2.322630138 1.211787008 H -5.777701979 1.682949028 .5218870262 H -7.113558914 2.376170457 1.155312156 O -5.740612474 -1.177654115 -1.730743481 H -5.096138763 -1.942025930 -1.750476108 H -6.264376114 -1.161427597 -2.582452562 O 4.079245822 -2.791226395 7.373513675 H 3.675370460 -3.227960377 6.569680277 H 3.988897405 -1.798495971 7.293993369 O -3.390377563 -3.599035053 -.4452659926 H -3.141708142 -3.390145874 -1.391061342 H -3.464039173 -2.748494714 .7545956937E-01 O .9925360025E-01 2.351666041 -.3061559128 H .7167995827 1.848484941 .2983651799 H .1262276512 1.948108546 -1.220712505 O 3.735588653 6.097333565 -4.188204031 H 4.201037481 6.368253226 -5.030795235 H 4.389151354 5.655068150 -3.573991437 O 3.620198578 2.256724618 -6.759037787 H 4.225394083 2.587421846 -7.483177106 H 4.167521710 1.966998785 -5.973864978 cell angstrom 15.0267420457 .0000000000 .0000000000 .0000000000 15.0267420457 .0000000000 .0000000000 .0000000000 15.0267420457 } # # All H-H's must be connected so that the topology generator # adds in the bond terms # for {set i 1} {$i <= 300} {incr i 3} { } # # vdw use 6/12 expression (replaces lennard-jones) # replace kj with kcal # read_input ff { vdw o o 628.841 633295.2 vdw o h .000000 0.000 vdw h h .000000 0.000 bond o h 100.0 1.1000 bond h h 1000.0 1.63288 charge o -0.82 charge h 0.41 } set tcl_precision 14 # # All H-H's must be connected so that the topology generator # adds in the bond terms # # Define neutral groups and constraints # set r1 [ expr 1.0 / 0.52917706 ] set r2 [ expr 1.63288 / 0.52917706 ] set con {} set grps {} for {set i 1} {$i <= 300} {incr i 3} { set h1 [ expr $i + 1 ] set h2 [ expr $i + 2 ] add_connection coords=c i = $h1 j = $h2 lappend con [list $i $h1 $r1 ] lappend con [list $i $h2 $r1 ] lappend con [list $h1 $h2 $r2] lappend grps [list $i $h1 $h2 ] } set dl_defs [ list \ mm_defs=ff list_option=none \ mxlist=5000 \ suppress_ewald=no ewald_precision=6 spme=yes \ ] matrix e energy coords=c theory=dl_poly : $dl_defs energy=e set final_energy [ get_matrix_element matrix=e indices= {0 0 } ] delete_object e delete_object c set etest -1.06030361 if { abs( $final_energy - $etest) > 1.0e-6 } { chemerr "Failed .. E= $final_energy, should be $etest" } else { return "OK" }