From a29bd84c670dfad173a6c6d44678c4592f3fec44 Mon Sep 17 00:00:00 2001 From: Josh D Littlefair Date: Thu, 30 May 2024 16:52:41 +0000 Subject: [PATCH] box stabilisation --- bin/openmmMD.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/openmmMD.py b/bin/openmmMD.py index 5953a55..7bd7a23 100755 --- a/bin/openmmMD.py +++ b/bin/openmmMD.py @@ -144,11 +144,11 @@ def md_nvt(simulation, csvname: str, totalsteps: int, reprate: int, pdbname, int simulation.context.setVelocitiesToTemperature(300*kelvin) simulation.reporters.append(app.PDBReporter(pdbname, reprate)) simulation.reporters.append(app.StateDataReporter(stdout, reprate, step=True, potentialEnergy=True, temperature=True, volume=True)) - prepdf = {'Step':[], 'Potential Energy (kJ/mole)':[], 'Temperature (K)':[], 'Box Volume (nm^3)':[], 'Pressure (kPa)':[]} + prepdf = {'Step':[], 'Potential Energy (kJ/mole)':[], 'Temperature (K)':[], 'Box Volume (nm^3)':[]} inidf = pd.DataFrame(prepdf) inidf.to_csv(csvname, index=False) simulation.reporters.append(app.StateDataReporter(csvname, reprate, step=True, - potentialEnergy=True, temperature=True, volume=True, density=True, pressure=True, append=True)) + potentialEnergy=True, temperature=True, volume=True, append=True)) simulation.step(totalsteps) final_state = simulation.context.getState(getEnergy=True, getPositions=True) final_pe = final_state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)