[gmx-users] ethanol solvation (equilibrated ethanol .gro file)

[Jashimuddin Ashraf]

Dear Gromacs users,

I want to create an ethanol solution to study CNT in ethanol dynamics. How
can I get/generate an equilibrated ethanol .gro file (like the
methanol216.gro or spc216.gro files)? I tried to use the genbox function
but the cannot get the density of the solution right.

Just to test my files, I ran a simulation of a box containing about 600
ethanols.
At the production MD, I came across this warning-
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The bond in molecule-type Ethanol between atoms 4 OH and 5 HH has an
estimated oscillational period of 9.0e-03 ps, which is less than 5 times
the time step of 2.0e-03 ps.

Maybe you forgot to change the constraints mdp option.
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The warning vanished as I reduced my time step by half. But inside my
md.mdp file I still had no constraints-
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OPTIONS FOR BONDS
constraints         = none
constraint-algorithm     = shake
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Am I doing anything wrong here? Any comment/suggestion would be very much
helpful for me.

Thanks in advance.