[gmx-users] decimal charge instead of integer

[Erik Marklund]

Carla Jamous skrev:
> 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
>
Well, if you removed one phosphate group you may not have removed 
exactly -1 e. What do the rtp-entries look like?

Erik
> 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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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys