[gmx-users] decimal charge instead of integer

[Justin A. Lemkul]

Carla Jamous wrote:
> Thank you Justin,
> but I ran a simulation before this one with GTP & it worked fine. GDP & 
> GTP parameters are identical except for GDP having less atoms.
> This is why I can't understand why I don't get an integer charge while I 
> did in my previous simulation.
> 

OK, but this still doesn't help anyone give you any advice.  Please refer to my 
previous post - which case applies to you: almost integer, or way off?

It is also potentially faulty logic to suggest that GDP parameters can be 
generated from GTP parameters by simply chopping off a phosphate.  Under most 
force field parameter sets, the charges on the beta-phosphate will have to 
change since the electronic properties of the molecule are now different.

-Justin

> Carla
> 
> On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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.
> 
>     -Justin
> 
>         Thanks
> 
>         Carla
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================