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Date:
2018-07-12 14:56
Priority:
3
State:
Open
Submitted by:
Nobody
Assigned to:
Nobody (None)
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.

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Comments:

Message  ↓
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.

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Field Old Value Date By
detailsAnonymous 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 16:55peastman
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