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Commit d0e168ad authored by peastman's avatar peastman
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Merge pull request #789 from swails/fixgb 

Fixgb
parents 8bd44206 91e353a8
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Showing with 57 additions and 57 deletions
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ d0e168ad
......@@ -217,7 +217,7 @@ def _createEnergyTerms(force, solventDielectric, soluteDielectric, SA, cutoff, k
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else:
if kappa > 0:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-kappa/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
force.addEnergyTerm("-138.935485*(1/soluteDielectric-exp(-kappa*f)/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
"f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))"+params, CustomGBForce.ParticlePairNoExclusions)
else:
force.addEnergyTerm("-138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*(1/f-"+str(1/cutoff)+");"
......@@ -380,4 +380,4 @@ def convertParameters(params, gbmodel):
newparams[i] = list(params[i])
newparams[i][0] -= offset
newparams[i][1] *= newparams[i][0]
return newparams
\ No newline at end of file
return newparams
wrappers/python/tests/systems/ala-ala-ala-implicit-forces/OBC2_NonPeriodic_Salt.xml
View file @ d0e168ad
......@@ -6,38 +6,38 @@
<C x="0" y="0" z="2"/>
</PeriodicBoxVectors>
<Forces>
<Force x="230.53816183034448" y="161.56808931034723" z="57.52342867705611"/>
<Force x="12.564077794922298" y="-.47807572311680246" z="-67.73089160911985"/>
<Force x="-138.11146161319016" y="-187.28762917098084" z="-128.55946321637822"/>
<Force x="-14.216667189461361" y="-184.42361950033217" z="-7.755578386971408"/>
<Force x="-51.715805944708976" y="-8.607643188725255" z="189.75546331479697"/>
<Force x="-92.82982967617171" y="-37.94701798925213" z="201.6270395366716"/>
<Force x="254.05585203757227" y="10.254599487982063" z="45.8494172596769"/>
<Force x="-27.659651768165375" y="8.348966087807838" z="-142.57089821391565"/>
<Force x="101.01881369689859" y="-109.75517229560455" z="-.21244790322278817"/>
<Force x="-21.38037204037586" y="22.86551289437265" z="-92.96600655235835"/>
<Force x="-397.09125537412" y="-424.17272961509434" z="135.01295191731154"/>
<Force x="156.04946355280902" y="705.0998513932067" z="-112.9041481108168"/>
<Force x="306.5652214156939" y="346.46968632209746" z="-27.505218241078808"/>
<Force x="-391.75561856075" y="-226.95233582000702" z="83.27667931906632"/>
<Force x="-2067.734655394289" y="-1129.4901474018056" z="-140.06254901471146"/>
<Force x="-191.13938275808238" y="-18.663742235265005" z="22.03099880659653"/>
<Force x="-729.4196877368092" y="-242.06033981478328" z="-550.7472953979611"/>
<Force x="-1061.6405049306088" y="-16.047501421098502" z="-835.6902589805981"/>
<Force x="-12.191029759977653" y="-71.33537155730633" z="-67.96942675367183"/>
<Force x="-3.4285805496120787" y="3.4221542613566953" z="-83.54534249560267"/>
<Force x="-535059.354506658" y="-759427.0708915488" z="-62607.30990893726"/>
<Force x="-865.6928542682272" y="-791.6607924296417" z="-636.7355970320627"/>
<Force x="-59134.540453248046" y="-11164.06852947624" z="4084.1721748771993"/>
<Force x="8523.705742783686" y="-5007.283077104953" z="201.13411363013654"/>
<Force x="-92085.95982714288" y="-81874.13444189396" z="-3131.0444535073093"/>
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<Force x="137691.52277938166" y="-29833.1218616508" z="13271.79861725629"/>
<Force x="-16859.409597911006" y="-20265.883709834423" z="-2793.2637780790105"/>
<Force x="-35331.66387798213" y="19901.063774262533" z="9356.077337288667"/>
<Force x="-6566795.1522480175" y="1625389.908741199" z="-3339649.746853593"/>
<Force x="8959758.524878602" y="469416.7061763106" z="202234.18939046844"/>
<Force x="-1344222.3868171684" y="1727597.777500562" z="3128292.1150764455"/>
<Force x="-1081153.1642807235" y="-3765540.083662639" z="-17383.96051482133"/>
<Force x="234.3570705217496" y="163.74358064335448" z="58.522749660942004"/>
<Force x="11.176275670899656" y=".10336043410973161" z="-67.8394884108773"/>
<Force x="-138.18399426699852" y="-188.63447670515973" z="-129.54908723981578"/>
<Force x="-15.57361985669769" y="-186.45874523275336" z="-6.747109759041365"/>
<Force x="-52.7674264281076" y="-8.800529541266094" z="189.15705938413362"/>
<Force x="-93.31172512294934" y="-38.325004897210775" z="201.00706349297002"/>
<Force x="256.65941343893945" y="11.602301514349506" z="45.95001464126818"/>
<Force x="-28.45807172055784" y="8.808219398965122" z="-143.27320686870036"/>
<Force x="100.23553999999972" y="-109.76252130988672" z="-.5879819608399757"/>
<Force x="-22.33472537289542" y="23.03629689095471" z="-93.47432259239747"/>
<Force x="-401.2968446685536" y="-430.4147340096256" z="135.16515833820998"/>
<Force x="160.8753607696059" y="710.1318948502379" z="-113.33155251450333"/>
<Force x="312.07346116178763" y="351.68193607795683" z="-26.997287485463573"/>
<Force x="-395.7366671447344" y="-228.51147888641327" z="83.07996301047257"/>
<Force x="-2068.7134151599125" y="-1129.9540145893047" z="-140.265674014711"/>
<Force x="-192.02003613943083" y="-19.583507707677057" z="21.378435711503514"/>
<Force x="-727.5540871508714" y="-242.96021164095555" z="-548.7788505737428"/>
<Force x="-1061.9428730946715" y="-16.510727739457792" z="-835.6965456016912"/>
<Force x="-12.590897771452802" y="-71.80267960173995" z="-67.66338694349132"/>
<Force x="-3.820990827932391" y="2.5665939586223203" z="-83.27820687548548"/>
<Force x="-535067.0613548026" y="-759426.2200156943" z="-62610.62216479664"/>
<Force x="-859.4142898151022" y="-789.8686781718292" z="-632.8392957625315"/>
<Force x="-59134.92697363379" y="-11169.742601741866" z="4087.8435921135274"/>
<Force x="8522.153260178706" y="-5005.082866533664" z="199.45333894141584"/>
<Force x="-92086.06708689325" y="-81874.16819052066" z="-3131.2773560341643"/>
<Force x="629671.515402093" y="832997.2817255558" z="70285.41316228079"/>
<Force x="137694.26325789728" y="-29834.67703743205" z="13273.511385810978"/>
<Force x="-16860.23015455163" y="-20265.776745723095" z="-2792.9598230008855"/>
<Force x="-35332.02002574824" y="19901.26715484725" z="9355.684799933244"/>
<Force x="-6566793.6522480175" y="1625390.283741199" z="-3339650.996853593"/>
<Force x="8959762.888403993" y="469418.38846543414" z="202231.72648458465"/>
<Force x="-1344222.6368171684" y="1727594.027500562" z="3128290.1150764455"/>
<Force x="-1081155.0392807235" y="-3765536.833662639" z="-17381.097965993205"/>
</Forces>
</State>
wrappers/python/tests/systems/alanine-dipeptide-implicit-forces/OBC2_NonPeriodic_Salt.xml
View file @ d0e168ad
......@@ -6,27 +6,27 @@
<C x="0" y="0" z="2"/>
</PeriodicBoxVectors>
<Forces>
<Force x="118.3535195440054" y="35.969449162483215" z="-.281414270401001"/>
<Force x="314.4263282418251" y="344.44179029762745" z="-.434397476259619"/>
<Force x="-1.4066988714039326" y="-49.76428470760584" z="-32.37674808874726"/>
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<Force x="-493.7057650089264" y="-643.0512407422066" z="398.3075271293055"/>
<Force x="7.296756054041907" y="-855.5627281765919" z="-257.9519661345985"/>
<Force x="-53.50385844707489" y="-24.334915697574615" z="-1.1155095011927187"/>
<Force x="429.9477740279399" y="379.88140909792855" z="60.92471059667878"/>
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</Forces>
</State>
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