[gmx-users] decimal charge instead of integer
Justin A. Lemkul
jalemkul at vt.edu
Thu Jan 21 14:26:12 CET 2010
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.
> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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