[gmx-users] Trifluoroethanol-Ethanol mixtures study

[Mark Abraham]

On 4/01/2011 9:39 AM, Marcelo Silva wrote:
> Hi everybody,
>
> I am starting to simulate ethanol-trifluoroethanol mixtures with opls 
> aa, but TFE is not defined in the opls rtp file, so I added a new 
> entry. I would like to confirm if the way the charge groups are 
> defined for ethanol are mantained for TFE:
>
> CB       1
> HB1    1
> HB2    1
> HB3    1
> CA      2
> HA1   2
> HA2   2
> OH     2
> HO     2
>
> Because in the case of TFE the charge groups don't add to zero.

Hence the charges are not assigned correctly. More is required than 
substituting OH for H in an ethane molecule, for a carbon with an 
electron-withdrawing group like -OH will have a more negative partial 
charge than the other carbon. TFE and ethanol will follow the same 
pattern of charge distribution, but with larger magnitudes for TFE.

>
> Also, would it be necessary to couple different thermostats to ethanol 
> and trifluoroethanol in mixtures from x=0 to x=1?

Certainly not. See 
http://www.gromacs.org/Documentation/Terminology/Thermostats

Mark