[gmx-users] decimal charge instead of integer
erikm at xray.bmc.uu.se
Thu Jan 21 14:25:07 CET 2010
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.
Well, if you removed one phosphate group you may not have removed
exactly -1 e. What do the rtp-entries look like?
> 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:
> 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 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
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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