From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Nov 17 2009 - 22:29:13 CST
NAMD initially defines the size of the periodic box using the cellBasisVector parameters in the input file. If you are simulating in the NVT ensemble, then the boundaries are fixed. If you are using a barostat, then whatever algorithm you choose will vary the size of the box to maintain a particular pressure. The references for the barostat algorithms are in the NAMD manual as is a description of the cellBasisVector parameters.
On Nov 17, 2009, at 11:16 PM, Michael Thomas wrote:
> Hi everyone,
> How does NAMD calculate the size of the periodic box during the simulation? Where exactly do the numbers for the box's vectors in the xst file come from?
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