[gmx-users] How to remove charge of 5e-2 ??

Mark Abraham mark.abraham at anu.edu.au
Wed Apr 6 09:22:23 CEST 2011

```On 06/04/11, mohsen ramezanpour  <ramezanpour.mohsen at gmail.com> wrote:
> Daer Dr.Mark
>
> You are right,But all of them(as I know) have integer charges!
> the problem is simullating a system with partial charges.
> We absolutely have such systems.
>

Read the other link I provided. 3.000003e00 indicates integer charge. One neutralizes it with a set of ions that have a net charge of -3.

Mark

> On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
>
> >
> >
> >
> >
> >
> >
> >     On 6/04/2011 4:45 PM, mohsen ramezanpour wrote:
> >
> > > Dear Dr.Justin
> > >
> > >
> > >
> > >       What can we do (how can neutralize system) if the total charge of
> > >       our system was not integer?
> > >
> > >       I think  there is not any solution and we have to simulate a
> > >       charged system not a neutral.
> > >
> > >       Am I right?
> > >
> > >
> >
> >
> >
> >
> >     I suspect every tutorial for simulating proteins in water deals with
> >     the need for counter-ions, and the technique for generating them.
> >
> >
> >
> >     Mark
> >
> >
> >
> >
> >
> > >
> > >       Thanks in advance
> > >
> > >
> > >
> > >       On Wed, Apr 6, 2011 at 11:12 AM, mohsen
> > >         ramezanpour <ramezanpour.mohsen at gmail.com>
> > >         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?!
> > > >
> > > >
> > > >
> > > >           What is your point of view?
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >               On Wed, Apr 6, 2011 at 3:40 AM,
> > > >                 Justin A. Lemkul <jalemkul at vt.edu>
> > > >                 wrote:
> > > >
> > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >                     김현식 wrote:
> > > > >
> > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >                        > Date: Tue, 5 Apr 2011 23:43:19 +1000
> > > > > >
> > > > > >                        > From: Mark.Abraham at anu.edu.au
> > > > > >
> > > > > >                        > To: gmx-users at 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
> > > > > >
> > > > > >                        > --
> > > > > >
> > > > > >                        > gmx-users mailing list gmx-users at gromacs.org
> > > > > >
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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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> > --
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