Error on the CP2K QM/MM tutorial on biochemical systems

QM/MM for Biomolecular Simulation
1

Hello,

I am running the QM/MM tutorial on chorismate mutate as posted on the CP2K webpage (www.cp2k.org/howto:biochem_qmmm). I managed to run the first steps including MM minimisation and MM equilibration (NVT and NPT). However, in the QM/MM monitor calculation, I encounter the following error after running 50 steps:

GEOMETRY wrong or EMAX_SPLINE too small!
fist_neighbor_lists.F:607

To solve this, I tried:

  • To increase the EMAX_SPLINE value but the error persisted.
  • I visualised the coordinates and trajectories and they seem to be correct.
  • using two versions of CP2K (v5 and v6).

I followed the steps described in the tutorial. I modified the Parmed commands to properly change the LJ parameters of the oxygen atoms. In my system, the correct atom identifiers were:
printDetails @5723
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth Mass Charge GB Radius GB Screen
5723 364 WAT O OW 8 1.7683 0.1520 16.0000 -0.8340 1.5000 0.8500
printDetails @4842
ATOM RES RESNAME NAME TYPE At.# LJ Radius LJ Depth Mass Charge GB Radius GB Screen
4842 299 SER OG OH 8 1.7210 0.2104 16.0000 -0.6546 1.5000 0.8500
changeLJSingleType :WAT@O 0.3019 0.047
changeLJSingleType :*@OG 0.3019 0.047

I also noticed that the temperature of the system is really high before crashing.
TOTAL TEMPERATURE[K] = 450.232
QM TEMPERATURE[K] = 495.914

Could you help me to sort this out?

I have attached: monitor input, output, topology and coordinate files to this threat:
CP2K input monitor.inp (3.5 KB)
CP2K output monitor.out.dat (246.3 KB)
Initial coordinates (XYZ) NPT-50000_time_25000.000_E_-269.1738741202.xyz.dat (3.1 MB)
Modified topology (gzip AMBER prmtop) complex_LJ_mod.prmtop.gz.dat (668.7 KB)

Thank you very much for your help!

Salomé

2

Hi Salome,

Your system seems to be exploding because the hydrogen atoms of water and serine are creating unphysical interactions with QM subsystem. This could be due to missing LJ parameters and the incorrect assignment of parameters for the all the water oxygens and OG atom types in the topology.
After topology correction the thermostat should stay stable during the QMMM calculation.

Cheers!
Modi

3

Hi Modi,

Thank you very much for your help.
I fixed my topology accordingly to your comments and it works. I just had to correct the LJ parameters of the hydrogen atoms of the water molecules and hydroxyl groups in parmed.

changeLJSingleType :WAT@H1 0.3019 0.047
changeLJSingleType :WAT@H2 0.3019 0.047
changeLJSingleType :*@HO 0.3019 0.047

Best,

Salomé