[gmx-users] Acetone parameters and transferability question

[Justin Lemkul]

On 10/12/14 5:38 AM, Ioanna Styliari wrote:
> Hello Justin, and thank you for your reply.
>
> Yes, the diffusion constant with the ATB acetone (code name _LVN) was
> overestimated in a variety of molar ratios (used SPC water), but also, I am
> not able to reproduce acetone's experimental density correctly (result was
> around 830 rather than 791 kg/m^3) When building the acetone-solvation boxes,

A 5% error is actually rather good.

> I have followed the guides from Gromacs. Another fact is that the second
> acetone model ATB has, (code name AON, a united atom model for the 53a5ff) is
> immiscible with water, possibly due to the very low charge in the C=O
> molecules. How can I be certain that the acetone model I use is OK? I am

The 53A5 parameters are for simulations in cyclohexane, not water, hence the 
insolubility is to be expected.

> trying to be as careful as possible but really need an expert's advice on
> which molecule to use.
>

If the density is only off by 5%, it should be reasonably easy to tweak the 
parameters.  To be in line with the existing force field, target data should 
also include heat of vaporization and solvation free energy.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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