When using the tclBCScript interface of namd for imposing additional forces on a classical molecular dynamics simulation, you may get the (undocumented) error message ------------- Processor 0 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: tclBCScript failed to call nextatom until failure Charm++ fatal error: FATAL ERROR: tclBCScript failed to call […]
namd2
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If you do NPT simulations with namd2, you may get the following message: FATAL ERROR: Periodic cell has become too small for original patch grid! Unfortunately, namd2 does not support automatic restarts in this case. Here is a small wrapper script, that automates this process. Just prepare your namd.conf as […]
In case you want to perform a relaxed scan of the potential energy surface for a given dihedral, you have to perform constrained (or at least restrained) optimizations. The namd way to do so is to define a collective variable (colvar in namd terminology) and then impose a harmonic potential […]
In case you get an error message of the form FATAL ERROR: Setting parameter binaryoutput from script failed! you should try moving the line specifying the parameter in question in your config file. In particular, the parameter has to preceed any command actually performing calculations. For example, this config file […]