[gmx-users] Modify charge groups

[Justin A. Lemkul]

parto haghighi wrote:
> Dear Justin,
> Thank you very much for your response.
> I have another question to continue my calculations.
> 
> To correct charges and charge groups I have to:
> 1) seprate the molecule to functional groups
> 2) some of these functional groups are already exist in selected force 
> field ( in aminoacid.rtp) with their charges, so as you said in fifth 
> tutorial  "life is pretty easy"

For a single (isolated, non-polymerized) molecule, there is no real need to 
build .rtp entries.  You can just construct an .itp file directly.  Either 
approach would work, I suppose, but there are online tools that write .itp files 
for you that can be modified.

> 3) for new functional groups I have to:
> 
>   i) do QM calculation
>  ii) calculate free energy of solvation or logP
> iii) compare simulation results with experimental data
> 
> my questions are when my simulation results do not have any consistence 
> with experimental data, how can I modify new functional groups? and how 
> can I decide which one of atoms have improper charge?
> 

Such is the difficulty of empirical parameterization.  If you're dealing with a 
small enough model compound, then it is trivial to see which components of the 
nonbonded energy (van der Waals or Coulombic terms) are too large or too small. 
  You can scale parameters as needed.  I have generally found that charges make 
the biggest difference, but really exotic molecules may require more extensive 
reparameterization of vdW or bonded terms.

-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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