[gmx-users] LINCS warnings for bonds that do not exist

My simulation aborts rather quickly because it accumulates too many LINCS warning. I checked the various plots and everything seems to be stable (temperature, pressure, total energy, etc.). The stderr gives me warnings looking like this: Step 2304252, time 4608.5 (ps) LINCS WARNING relative const

[gmx-users] GROMPP replaces lipid atom coordinates with these of water molecules

Hello, I have been running a simple simulation where I replace 150 water molecules in a waterbox with a lipid called DPC to create micelles. This simulation is working fine and I'm getting decent micelles fairly quickly. I am now trying to do the same, but with a small peptide in the simula

[gmx-users] FFT plan mismatch with mdrun_mpi

Hello, I'll first apologize in case that this is a common issue with an available solution, but I have a problem running mdrun_mpi on a rock cluster and there is no amount of searching that I can do to find information on this error (manual, online docs, general google search). Could someone point