GROMACS

I had problems with unexpected LINCS errors appearing in my simulation of a protein dimer in water+NaCl. The error only occurred with group cutoffs, however. I eventually discovered that the SOL-SOL short-range potential energy was zero with the group cutoff, but not with the verlet cutoff. amber99sb-ildn and tip4p-Ew was used to model the system.

Here are the energies after a few em steps with verlet and group kernels, respectively. mdp files are nearly identical:

[marklund@ajbchap3 em2]$ diff em_group.mdp em.mdp
72c72
< cutoff-scheme            = group
---
> cutoff-scheme            = verlet
100c100
< vdw-modifier             = Potential-shift
---
> vdw-modifier             = Potential-shift-verlet

group
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:SOL-SOL                   0          0       -nan          0  (kJ/mol)

verlet
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:SOL-SOL             -948221      15000      32896    -104103  (kJ/mol)