[gmx-users] decimal charge instead of integer

[Carla Jamous]

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.

Carla

On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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