Potential NAMD Update Bug

From: Shiv Seshan (sseshan_at_uchicago.edu)
Date: Fri Jun 25 2021 - 15:17:43 CDT


I am a student researcher simulating the dynamics of TIP4P water within solvated protein systems. When I used NAMD 2.14 to minimize the energy of a solvated system containing the 1UBQ protein (using the appropriate topology, parameter, PDB, and PSF files), I received the following error message: "FATAL ERROR: Must have the same number of LP hosts as lone pairs." However, when I used an older version of NAMD--NAMD 2.12--to minimize the energy of the same system (with the same topology and parameter files), the minimization was successful. Is this a result of a bug in NAMD 2.14? Can I trust the output of the minimization program I ran on NAMD 2.12?


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