[gmx-users] Lincs constraints failure

[Mark Abraham]

Hi,

What are you exchanging between replicas? Seems like the most likely issue.

Mark

On Sat, 24 Jun 2017 16:50 Qinghua Liao <scorpio.liao at gmail.com> wrote:

> Hello,
>
> I have searched on Google for the LINCS warning problems, and there are
> already many discussions,
> but I guess that my situation might be different.
>
> I have a system of protein/micelles/water_ions in a dodecahedral water
> box. The system is fully equilibrated by several steps.
>
> 1. minimizations (steep, cg) with positional restraints (1000 kJ/mol
> nm2) on protein and micelles,
> 2. 500 ps NVT equilibration, time step 1 fs, positional restraints (1000
> kJ/mol nm2) on protein and micelles,
> 3. 500 ps NPT equilibration, time step 1 fs, positional restraints (1000
> kJ/mol nm2) on protein and micelles,
> 4. 500 ps NPT equilibration, time step 1 fs, positional restraints (800
> kJ/mol nm2) on protein and micelles,
> ...500 ps, restraints, 600 kJ/mol nm2, 1fs
> ...500 ps,  restraints, 400 kJ/mol nm2, 1fs
> ...500 ps restraints, 200 kJ/mol nm2,  1fs
> ... 500 ps restraints, 100 kJ/mol nm2, 1 fs
>
> 5. 15 ns equilibration, positional restraints (100 kJ/mol nm2) only on
> protein, letting the micelles assemble, time step 1 fs
> 6. 5 ns MD simulation, without any restraints, time step 2 fs
>
> For all these steps, the constraints were applied to h-bonds, which is
> the same for following simulations.
> And the I started a Hamiltonian replica exchange simulation, 4 replicas
> were chosen, time step is 2fs.
> But the simulation crashed at the simulation time of 25 ns. The error is
> shown like:
> #
> step 12855987: Water molecule starting at atom 66929 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
> #
> Step 12855991, time 25712 (ps)  LINCS WARNING in simulation 3
> relative constraint deviation after LINCS:
> rms 0.000678, max 0.010615 (between atoms 3541 and 3542)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>     3541   3543   90.0    0.1010   0.1020      0.1010
> #
>
> Atom 3541 is ND2 of ASN227, and atom 3543 is HD22 bonded to atom 3541. I
> checked the trajectory file, and I didn't find Asn227 doing something
> improperly.
>
> I also found that the constraints failure happened faster if I used 2 fs
> with constraints for all bonds. I believe that a time step of 1 fs will
> work, which also means
> more computing time since the system is very big. Any suggestions?
> Thanks very much!
>
>
>
> All the best,
> Qinghua
>
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