[gmx-users] decimal charge instead of integer

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 21 14:15:55 CET 2010

Carla Jamous wrote:
> Hi,
> In order to run my simulation, I had to insert GDP parameters in 
> ffamber94 (the force field I'm using).
> However, I'm having a problem with GDP charge.
> the charge of every charge group in top file should be an integer. But 
> I'm getting a decimal charge which gives me naturally a decimal total 
> charge of my molecule.
> I checked number of atoms, it's correct, their charge also.
> But it seems it's having trouble adding charges & giving an integer charge.
> Does anyone have an idea where is the source of the problem?

What is the charge?  If it is a small difference between an integer and your 
charge (i.e., the difference between +1.9999 and +2) then there is no problem. 
The issue there is the inherent limitation of doing a lot of floating-point 
operations to sum the total charge.  If, however, you have a charge of +1.9256 
when you wanted +2, then your parameters are simply wrong.


> Thanks
> Carla


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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