[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?
> > > >
> > > > Thanks in advance for your reply
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > 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
> > > > > >
> > > > > > > --
> > > > > >
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> > > > > >
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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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