[gmx-users] free energy and charges

[Justin A. Lemkul]

parto haghighi wrote:
> Dear GMX users,
> 
> when I want to correct charge group of one molecule I have to do 
> calculate its free energy.
> I did this work by applying 6th gromacs tutorial.
> In this tutorial user has to assign 0 value in topology:
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB  massB
>      1   opls_138      1   ALAB     CB      1      0.000       12.011   
>      2   opls_140      1   ALAB    HB1      2      0.000       1.008   
>      3   opls_140      1   ALAB    HB2      3      0.000       1.008   
>      4   opls_140      1   ALAB    HB3      4      0.000       1.008   
>      5   opls_140      1   ALAB    HB4      5      0.000       1.008   
> 
> 
> my question is when I have to zero value to its charge how can I correct my charges:
> 

Don't set your charges to zero.  The tutorial states why everything is zero 
there - the process for which the free energy calculation is being done is a van 
der Waals transformation, so the charges are fixed at zero.  For your 
calculations, you need to:

1. assign some starting value for charges (QM, chemical intuition, etc) and atom 
types
2. calculate DG of solvation and check the accuracy of the resulting value
3. adjust charges (and perhaps atom types) if necessary and return to step 1

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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