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Bug #1426

Updated by Mark Abraham about 6 years ago

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:

<pre>[marklund@ajbchap3 [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)</pre> (kJ/mol)

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