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
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