[gmx-users] How to remove charge of 5e-2 ??
ramezanpour.mohsen at gmail.com
Wed Apr 6 08:42:36 CEST 2011
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!
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
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
>> > >
>> > > 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.
> Thank you,
>> > 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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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