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

Mohamed Abdelaal m.b.abdelaal at gmail.com
Thu May 7 13:22:10 CEST 2020

Many thanks Alex for your reply :)

You have pressure scaling and LINCS convergence issues, suggesting that
> the starting configuration is far from equilibrium, as well as
> potentially other issues.
> How to check if my starting configuration is far from equilibrium ? I
checked the Temperature and Pressure curves ( attached in the original
email) and they look equilibirated. Is there anything I am missing?

> 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.

How can I make that my graphene edges are crystallographically commensurate
with respect to PBC ?

I have chosen box size equal to the graphene sheet size and increased the
height to make sure that the deposited molecules will not be deposited out
of my graphene sheet area.

> Finally, make sure that the small molecules you're
> depositing on graphene are properly pre-equilibrated.
> Actually, after your email, I did the simulation for both the graphene
sheet and the deposited molecules (C60) each alone to check with one has
problems with the lincs warning. The C60 alone was successfully completed.
The Graphene sheet didn't work due to the lincs warning. I know now that
the problem is only in the graphene sheet.

> Alex

> 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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