[gmx-users] Re: Carbon Nanotube Simulation Issues

[Mark Abraham]

> running grompp I use the following command:
> grompp -f mdout_test.mdp -c SWNT_6_6_144_b4em.gro -p SWNT_6_6_144.top
> -maxwarn 10000 -pp
>
> It works but there is 1176 warnings, which I am assuming this is a
> problem?

Yes.

> Then I run mdrun using the following command:
> Mdrun -s topol.tpr
> It works just fine
> Then I can view it with ngmx using the following command:
> ngmx -f traj.xtc -s topol.tpr.
> This works just fine as well.

Adding together two random numbers gives you a random result, but this
doesn't mean anything either :-)

> My question is are the warnings ok/normal or is there some fix that needs
> to
> be made?

No and yes, respectively.

Mark