[gmx-users] Lincs warning and Bond length not finite

Alex nedomacho at gmail.com
Mon May 4 03:03:57 CEST 2020

You have pressure scaling and LINCS convergence issues, suggesting that 
the starting configuration is far from equilibrium, as well as 
potentially other issues.

Gromos FF is not appropriate for graphene, and neither is turning C-C 
bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is 
not a small organic molecule or a protein. Also, if your system is 
periodic in all directions, make sure the graphene edges are 
crystallographically commensurate with respect to PBC and the box size 
is appropriate. Finally, make sure that the small molecules you're 
depositing on graphene are properly pre-equilibrated.


On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote:
> Hello everyone,
> I am simulating  the evaporation of non protein molecules on a graphene
> sheet. I am using gromos force field and hence the lincs constrain are set
> to all-bonds.  I have done the energy minimization and NVT
> successfully without any warnings. During the NPT equilibiration I got
> Lincs warning but the NPT equilibiration was completed to the end. During
> the md production run, I received lincs warning and Bond length not finite
> and sometimes I received " nonbonded interaction between particles is
> larger than the table limit 2.437 nm".
> I have read that this means that my system is blowing up. Hence, I have
> read the Blowing up and diagnosing unstable system  on gromacs website, I
> can't recognize  any of the posted issues in my files/simulation and
> hence,  I can't decide what exactly is the problem or what should I change
> (it seems that my system is well minimized and the temperature and pressure
> looks fine). I have added in the below link, the NPT and md logs  and .mdp
> files and pictures for the potential energy, Temperature, Pressure and
> Density.
> https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF
> I have tried the simulation again with none as  lincs constrains and it
> worked without any errors.
> I think the problem has something to do with the pressure since the problem
> started during the NPT, but I don't know how exactly to find the problem.
> Can anyone guide me please what should I change or how should I start ?
> Thanks,
> Mohamed

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