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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| from charmm import apocharmm as ch | ||
| import argparse | ||
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|
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| def p21_bilayer(): | ||
| prm = ch.CharmmParameters( | ||
| [ | ||
| "../test/data/par_all36_lipid.prm", | ||
| "../test/data/toppar_all36_lipid_cholesterol.str", | ||
| "../test/data/toppar_water_ions.str", | ||
| ] | ||
| ) | ||
|
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| filePath = "/v/gscratch/mbs/spark/induced-order/test_p21_apo_charmm/sq2x2/low/" | ||
| psf = ch.CharmmPSF(filePath + "init.psf") | ||
| # minimized for P21 | ||
| crd = ch.CharmmCrd(filePath + "step6.6_equilibration.crd") | ||
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| fm = ch.ForceManager(psf, prm) | ||
| fm.setBoxDimensions([144.96, 144.96, 98.65]) | ||
| fm.setFFTGrid(150, 150, 108) | ||
| fm.setKappa(0.34) | ||
| fm.setCutoff(14.0) # cutnb of CHARMM | ||
| fm.setCtonnb(10.0) | ||
| fm.setCtofnb(12.0) | ||
| fm.setPeriodicBoundaryCondition(ch.P21) # Only for P21 simulations | ||
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| ctx = ch.CharmmContext(fm) | ||
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| ctx.setCoordinates(crd) | ||
| ctx.assignVelocitiesAtTemperature(300) | ||
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| langevinThermostat = ch.LangevinThermostatIntegrator(0.002) | ||
| langevinThermostat.setFriction(12.0) | ||
| langevinThermostat.setBathTemperature(298.17) | ||
| langevinThermostat.setSimulationContext(ctx) | ||
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| subscriber = ch.DcdSubscriber("out/p21_soohyung_nvt_new.dcd", 1000) | ||
| # restartsubscriber = ch.RestartSubscriber("out/p21_soohyung_nvt.res", 10000) | ||
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| langevinThermostat.subscribe([subscriber]) # , restartsubscriber]) | ||
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| numSteps = int(5e4) | ||
| langevinThermostat.propagate(numSteps) | ||
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| langevinPiston = ch.LangevinPistonIntegrator(0.002) | ||
| langevinPiston.setCrystalType(ch.CRYSTAL.TETRAGONAL) | ||
| systemMass = psf.getMass() | ||
| pistonMass = 0.05 * systemMass | ||
|
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| langevinPiston.setPistonMass( | ||
| [pistonMass, pistonMass]) # 2 values for x/y and z | ||
| langevinPiston.setPistonFriction(20.0) | ||
| langevinPiston.setBathTemperature(298.17) | ||
| langevinPiston.setSimulationContext(ctx) | ||
|
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| """ | ||
| restartsubscriber = ch.RestartSubscriber("old.res", 10000) # an already existing restart file | ||
| langevinPiston.subscribe([restartsubscriber]) | ||
| restartsubscriber.readRestart() | ||
| """ | ||
|
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| baseName = f"out/p21_soohyung_npt_new_{0.002}_{20.0}_{pistonMass}" | ||
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| dcdSubscriber = ch.DcdSubscriber(f"{baseName}.dcd", 1000) | ||
| restartsubscriber = ch.RestartSubscriber(f"{baseName}.res", 10000) | ||
| # stateSub = ch.StateSubscriber(f'{baseName}.state', 1000) | ||
| # stateSub.setReportFlags("all") | ||
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| # langevinPiston.subscribe([subscriber, restartsubscriber, stateSub]) | ||
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| langevinPiston.subscribe([dcdSubscriber]) # , restartsubscriber]) | ||
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| nptSteps = int(5e6) | ||
| langevinPiston.propagate(nptSteps) | ||
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| if __name__ == "__main__": | ||
| """ | ||
| parser = argparse.ArgumentParser(description="P21 bilayer simulation") | ||
| parser.add_argument("timeStep", type=float, help="Time step value") | ||
| parser.add_argument( | ||
| "frictionCoefficient", type=float, help="Friction coefficient value" | ||
| ) | ||
| parser.add_argument( | ||
| "pressurePistonMassFactor", | ||
| type=float, | ||
| help="Pressure piston mass factor : X default value", | ||
| ) | ||
| parser.add_argument( | ||
| "temeperaturePistonMassFactor", | ||
| type=float, | ||
| help="Temperature piston mass factor : X value", | ||
| ) | ||
| args = parser.parse_args() | ||
| """ | ||
|
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| p21_bilayer() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,32 @@ | ||
| // BEGINLICENSE | ||
| // | ||
| // This file is part of chcuda, which is distributed under the BSD 3-clause | ||
| // license, as described in the LICENSE file in the top level directory of this | ||
| // project. | ||
| // | ||
| // Author: Samarjeet Prasad | ||
| // | ||
| // ENDLICENSE | ||
|
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| #pragma once | ||
|
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| #include "ForceManager.h" | ||
| #include "Subscriber.h" | ||
| #include <fstream> | ||
|
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| /** @brief Linked to several ForceManager objects. When reporting, asks each FM | ||
| * to compute energy and reports it along with the actual CharmmContext FM. */ | ||
|
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| /** @brief Reports the enegy of every single ForceManager child */ | ||
| class EDSSubscriber : public Subscriber { | ||
| public: | ||
| EDSSubscriber(const std::string &fileName); | ||
| EDSSubscriber(const std::string &fileName, int reportFreq); | ||
| void update() override; | ||
| ~EDSSubscriber(); | ||
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| private: | ||
| void initialize(); | ||
| int numFramesWritten; | ||
| std::vector<std::shared_ptr<ForceManager>> fmlist; | ||
| }; |
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