[gmx-users] Still :Partial charges QM to GROMACS

[Justin A. Lemkul]

The derivation of Gromos96 parameters started with some QM, but only to get the 
electron densities, if I remember correctly.  The QM charges were never used. 
The partial charges were assigned to each atom empirically using a reasonable 
guess based on the electron densities from QM, and adjusted as part of the 
parameterization scheme.

As such, I don't know that there is a 100% clear answer here.  Using the QM 
charges is not going to help you...directly.  As I said previously, probably the 
best way to do this parameterization would be empirical derivation, basing your 
charge assignment on the functional groups already present in the Gromos96 force 
field.

Alkyl chains are uncharged in this force field, but aromatic C-H bonds do have 
small partial charges (-0.140 for C, 0.140 for H in 53a6).  The thing that you 
have to be careful of is charge groups, which generally contain a total integer 
charge over 2 or 3 atoms, something that is not likely to work directly from 
QM-derived charges.

-Justin

nahren manuel wrote:
> Dear Gromacs Users, 
> 
> I think I did not frame my question correctly tha last time around. 
> Sorry. Lets say for a C-H (alkyl) bond the partial charges ( from 
> SEMI-EMPIRICAL) are (in bracket) ....C(0.234)-H(0.045) . so when I am 
> using united atom ff such as GROMOS96 should I take the partial charges 
> on carbon as sum of partial charges on C and H (which im my eg becomes 
> 0.234 + 0.045 =0.279), ??
> 
>  
> 
> regards,
> 
> nahren
> 
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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