[gmx-users] How to remove charge of 5e-2 ??
Erik Marklund
erikm at xray.bmc.uu.se
Wed Apr 6 09:23:48 CEST 2011
Hi,
No we don't. You can't have fractions of elementary particles in your
molecules.
Erik
mohsen ramezanpour skrev 2011-04-06 09.13:
> 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.
>
> On Wed, Apr 6, 2011 at 11:22 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
>> <mailto: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 <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> ??? wrote:
>>
>>
>>
>> > Date: Tue, 5 Apr 2011 23:43:19 +1000
>> > From: Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>
>> > To: gmx-users at gromacs.org
>> <mailto: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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>>
>> --
>> ========================================
>>
>> 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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--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://folding.bmc.uu.se/
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