[Periodic Boundary]: from charmm to namd

From: Sascha Tayefeh (sascha_at_pc.chemie.tu-darmstadt.de)
Date: Tue Nov 02 2004 - 09:08:42 CST

Dear Community,

 I have continuously encountered the same problem with many systems
created with charmm, and this is:

 Supposing, I have used an orthorombic cell in charmm for periodic
boundary (pb), I would have to use significantly higher values for cell
dimensions in order to make this system run with namd. However,
initially working with a canonic ensemble, I may not change
cell-dimensions during namd-run.

 I have realized, that the order, of which the dimensions need to be
increased are the same as the atoms of the molecules that were not
wrapped, anyway, if so, why does namd not (or falsely?) realize wrapped
atoms? Or better:

 How can I use same cell dimensions in namd I used in charmm?


 Sascha T.

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