[gmx-users] Lincs constraints failure

[Qinghua Liao]

Hello Mark,

Thanks a lot for your reply! I performed Hamiltonian replica exchange 
simulations,
the Hamiltonians (LJ, electrostatic, dihedrals ) of certain residues 
were scaled for exchange  between replicas.

You mean this kind of constraints failure is quire common in replica 
exchange? Apart from using smaller time step (i.e. 1 fs),
is there some other solution? Thanks a lot!


All the best,
Qinghua

On 06/25/2017 09:04 PM, Mark Abraham wrote:
> 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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