[gmx-users] Water molecule cannot be settled

[Andrew Beevers]

I have been attmpeting to perform both steepest descent energy minimisation and MD upon a DMPC lipid bilayer containing water molecules.

At each attempt I am confronted with the same error message which is:

water molecule at position "X" cannot be settled, check for bad contacts or reduce timestep. (X being an integer)

This has been reported at both timesteps of 2fs and 1fs and I have removed all water molecules from the pdb file that appear to be in unstable environments (i.e. inside or close to the bilayer area). Is there any other procedure possible to correct this problem?

Dr Andy Beevers
University of Warwick
UK