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

[Mohamed Abdelaal]

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