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:
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
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 ?
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