[gmx-users] partial charge distribution

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 25 12:42:16 CET 2008

Manik Mayur wrote:
> Hi,
> I have a system (a slit type nanopore) in which I have 4 wall layers. I 
> would like to distribute partial charges on the first wall layer (the 
> layer in contact with the fluid). The wall layers are made of Si atoms. 
> I tried to change ffG43a1nb.itp (& ffG43a1.atp) by adding a new atom 
> with characteristics of Si and with the required partial charge, but saw 
> that even for the ions the charge mentioned there is 0. So, my questions 
> are-
> 1) Where is the charge information stored?

If you're trying to create a topology using pdb2gmx, then such information 
should be in the .rtp file.

> 2) Will adding a new atom in the ff*tp files won't break anything and I 
> should proceed with that? Any other suggestion is also welcomed.

I don't see why it was necessary; Si is already part of ffG43a1, unless you are 
trying to create new parameters for use with your particular case.  But no, 
nothing should be broken if you've simply added an atom type and its nonbonded 
parameters.  If the Gromacs tools don't recognize the information, it should be 
ignored (provided that all the information was entered in the correct format).


> Merry christmas,
> Manik
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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