Hi all,
I have encountered problems with the interface between GROMACS and CP2K. I setup my calculation standardwise for GROMACS and did the whole standard procedure, minimization, NVT equilibration and NPT equilibration. After that I want to do QM/MM dynamics with NPT-ensemble for my system. The force fiield I used was OPLS, and the water model was tip4p. The time step was 2 fs.
The first problem is related to the generation of tpr files. As you can see, if you put in the bond parameters,
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
Then you will get the following warning:
“WARNING 1 [file md.mdp]:
Your QM subsystem has a lot of constrained bonds. They probably have been
generated automatically. That could produce an artifacts in the
simulation. Consider constraints = none in the mdp file.”
If you select none instead of hbonds in constraints, then the calculation will fail after several step. In this case after 6 steps.
“step 6: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates”
When you make the time-step smaller, then the calculation will run a bit longer but also fail after some steps.
“step 156: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates”
I tried to redo the simulation with AMBER force field. The same error occured after 345 steps.
My question is:
- will the constraints be applied on the QM subsystem, so that I can ignore the warning?
I try to modify the LJ-Parameter as the CP2K QMMM tutorial suggested.
With OPLSFF the calculation just failed because the potential energy is just too high.
“Step 0: The total potential energy is 1.33998e+17, which is extremely high.
The LJ and electrostatic contributions to the energy are 1.33998e+17 and
-107853, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.”
With AMBERFF, the calculation fails at the first step, and gave the same mistake “step 0: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.”
So basically I think the problem with water settling is not related with the parameters itself but rather with the constraint.
Unfortunately, as a new user, I cannot attach my input files here.
Best regards