[gmx-users] How to remove charge of 5e-2 ??
Erik Marklund
erikm at xray.bmc.uu.se
Wed Apr 6 10:00:34 CEST 2011
mohsen ramezanpour skrev 2011-04-06 09.31:
>
>
> On Wed, Apr 6, 2011 at 11:53 AM, Erik Marklund <erikm at xray.bmc.uu.se
> <mailto:erikm at xray.bmc.uu.se>> wrote:
>
> Hi,
>
> No we don't. You can't have fractions of elementary particles in
> your molecules.
>
> Dear Erik
>
> Yes,You are right.It is obvious .
> But I wanted to simulate a part of my system.for example a part of my
> protein!
> I was wrong,we can't do that
>
I think there are several examples of that in literature, e.g. by Åqvist
and coworkers. But think they use a different approach than just cutting
away part of the protein.
Erik
>
> 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 <mailto:erikm at xray.bmc.uu.se> http://folding.bmc.uu.se/
>
>
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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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