SimTK: OpenMM: [#2672] MonteCarloBarostat periodic box vector change reflected in simulation.topology

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Date:
2018-07-12 14:56

Priority:
3

State:
Open

Submitted by:
Nobody

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Summary:
MonteCarloBarostat periodic box vector change reflected in simulation.topology

Detailed description
Anonymous message posted by hd16974@bris.ac.uk I have an OpenMM script which runs a simulation using a MonteCarloBarostat, so naturally, my periodic box sizes at the beginning and end of the simulation are different. However, I use PDBFile to write out my system and the simulation.topology I pass to it writes out the earlier unit cell vectors - even after the barostat has changed the box size. This leads to gaps between my periodic boxes. I have gotten around this by passing the new periodic box size information from my context to Topology.setUnitCellDimensions(), however, I wondered if it might be prudent to give users the option of automatically updating this periodic cell information when using a barostat to change box size. Thanks.
Anonymous message posted by hd16974@bris.ac.uk I have an OpenMM script which runs a simulation using a MonteCarloBarostat, so naturally, my periodic box sizes at the beginning and end of the simulation are different. However, I use PDBFile to write out my system and the simulation.topology I pass to it writes out the earlier unit cell vectors - even after the barostat has changed the box size. This leads to gaps between my periodic boxes. I have gotten around this by passing the new periodic box size information from my context to Topology.setUnitCellDimensions(), however, I wondered if it might be prudent to give users the option of automatically updating this periodic cell information when using a barostat to change box size. Thanks.

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Date: 2018-07-12 16:55 Sender: Peter Eastman The PDB format doesn't support varying the box size over a simulation. It only provides one place to store a single box size for the whole trajectory. If you write to a DCD file instead, it will record the current box vectors for each frame. Remember that a Topology isn't specific to a Simulation. You can create many different Simulations that all use the same Topology, so automatically modifying it would create many potential bugs.

Field	Old Value	Date	By
details	Anonymous message posted by hd16974@bris.ac.uk I have an OpenMM script which runs a simulation using a MonteCarloBarostat, so naturally, my periodic box sizes at the beginning and end of the simulation are different. However, I use PDBFile to write out my system and the simulation.topology I pass to it writes out the earlier unit cell vectors - even after the barostat has changed the box size. This leads to gaps between my periodic boxes. I have gotten around this by passing the new periodic box size information from my context to Topology.setUnitCellDimensions(), however, I wondered if it might be prudent to give users the option of automatically updating this periodic cell information when using a barostat to change box size. Thanks.	2018-07-12 16:55	peastman

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