김현식 wrote:
> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] How to remove charge of 5e-2 ??
>
> On 5/04/2011 11:17 PM, Hyunsik wrote:
> > Dear experts,
> >
> > Hi,
> >
> > When prepare a system, the system had +5.5. So I add 5 CL- ion to
neutralize.
> >
> > But as you know, the Cl charge is -1 and there still is 5e-2. how
can i remove that.
>
> Your statements are inconsistent. If you had 5.5 charge and added five
> chloride ions, you could not end up with 0.05.
oh.. I have mistaken.. I had 5.005 of the system charge.
So even if added five choride ions, the system charge is not zero.
there was 0.005
that is partial charge?? If like that, topology is broken or
something wrong? abnormal??
Maybe, maybe not. Rounding errors could account for this difference, especially
if your system is very large. Still, you should inspect your
topology/topologies for inconsistencies. If pdb2gmx created the topology, keep
an eye on the "qtot" column for a running total of the charge. If you've made
or adjusted any topologies on your own, double-check your work. If everything
looks correct, then the difference is likely a consequence of floating-point
math and nothing more.
-Justin
Thank you,
Hyun
>
> Mark
> --
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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
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