Fix solvating with truncated octahedral cells#1174
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drroe merged 21 commits intoAmber-MD:masterfrom Mar 27, 2026
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March 23, 2026 15:41
…rynnikov and Stephan Schott.
…o 0.0 to 1.0 range.
… be equal for truncoct
… looking trunc oct cells
…ation (thanks to N. Skrynnikov for the fix). Also enables truncated octahedron for 'nsolvent' keyword.
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V7.5.0
The code in LEaP had a bug in it which made it not scale up the truncated octahedral cell enough. This was OK for small systems, but as system size increased the unit cell would eventually become too small to properly encapsulate the solute. Here is an example for the PDB ID 1JJ2:
Nikolai Skrynnikov from Purdue identified this bug in LEaP and corrected it. This PR employs this fix so that truncated octahedral cells properly encapsulate the solute no matter what the size:
This PR also enables
truncoctsolvation with thensolventkeyword for the build command.This also adds a hidden keyword to the
minimageaction,tofacewhich is for calculating the closest distance to the center of any unit cell face, but this is mainly intended for debugging.