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

[Justin Lemkul]

On 3/15/15 8:26 AM, Jashimuddin Ashraf wrote:
> 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.
>

The density of the output from genbox depends on how you set the box.  Perhaps 
it won't be able to add all of the requested molecules, in which case you need a 
larger box and suitable equilibration.  The density during the simulation is 
also a function of the quality of the force field parameters.

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

Constraining bonds involving H is standard practice for just about every MM 
force field.  See discussion in the manual.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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