[gmx-users] False Atommass and charge?

Justin Lemkul jalemkul at vt.edu
Sun Mar 23 02:51:19 CET 2014

On 3/22/14, 3:39 PM, GtrAngus wrote:
> Hi there,
> I am trying to simulate a membrane but for now I kept it simple and I just
> have a box full of water. Now I want to calculate the polarisation density P
> = Q * R. Q is the charge and R the distance between two atoms in a molecule
> (here O-H ).
> Getting the distances is fine but I had troubles with the charge. It is way
> so small, something about E-33. So I got curiose and tried the atommasses
> and they are also too small....
> Here is the code I wrote in C :
> Any idea what is wrong? Because the manual suggests the "normal" SI units.

There is no text pasted above.  Charges should be accessible from a t_atom 
within the global topology, i.e. top->atoms.atom[i].q is the charge on atom i.

To get better advice, you'll need to provide the exact input and output.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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