On 6/04/2011 4:42 PM, mohsen ramezanpour wrote:
Dear Dr.Justin
I had the same problem.
I modified the charges and charge groupsin the topology of a drug.the
net charge of it is zero(I am sure)
though,when I used pdb2gmx it resulted a NOTE like the following:
NOTE:The system has non-zero total charge: 3.000003e00
I continued simulation and ignored it!
Because:
1- I checked my protein.top and qtot was 3
2-the net charge of my drug was 0
3-Besides,all charges have 3 digit precision,How can it have 0.000003
additional charge?!
See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
Mark
What is your point of view?
Thanks in advance for your reply
On Wed, Apr 6, 2011 at 3:40 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
κΉνμ wrote:
> Date: Tue, 5 Apr 2011 23:43:19 +1000
> From: mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
> To: gmx-users@gromacs.org <mailto: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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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