Re: [gmx-users] genion problem with divalent ions

[Leandro Bortot]

Hi there,

 In addition to setting -pq to 2 as Justin said, you can set -conc to a
very low value such as 0.1 for neutralizing the system.

 One more thing... genion apparently uses the box volume when
determining how many ions are necessary for getting a given ionic strength.
 However, depending of your system size and shape and box type the volume
of the protein may be considerable. Maybe the number of water molecules,
instead of the box volume, is a better criterion for determining the number
of ions to be added.

best regards,
Leandro

2012/9/9 Matthias Ernst 

> Hi,
>
> I just encountered (another) strange thing with genion.
> I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
> forcefield amber99sb), so I expected half of the system charge (-52) to be
> added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26
> which would be needed for neutralization. The same holds for Zn or Ca ions,
> which also are divalent in ions.itp
>
> Could it be that the routines of genion to determine the number of ions
> are not working properly? I mean, the -neutral option also does work only
> if the -conc flag is also there and provides a value > 0.0 (which in fact
> is not what I want when I just want do neutralize my system by adding
> ions...)
>
> Does anyone of you also had similar problems?
>
> Thank you,
> Matthias
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Re: [gmx-users] genion problem with divalent ions

[Justin Lemkul]

On 9/9/12 7:53 AM, Matthias Ernst wrote:

Hi,

I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
forcefield amber99sb), so I expected half of the system charge (-52) to be added
as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26 which would
be needed for neutralization. The same holds for Zn or Ca ions, which also are
divalent in ions.itp



Charge is not read from ions.itp, it is taken from the command line.  The value 
of -pq is 1, so if you're adding divalent metals, set it to 2.



Could it be that the routines of genion to determine the number of ions are not
working properly? I mean, the -neutral option also does work only if the -conc
flag is also there and provides a value > 0.0 (which in fact is not what I want
when I just want do neutralize my system by adding ions...)



This has been an issue for a long time.  I suppose no one has ever filed a 
redmine issue for it, so please do.  Otherwise, it won't get fixed.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] genion problem with divalent ions

[Matthias Ernst]

Hi,

I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 
2, forcefield amber99sb), so I expected half of the system charge (-52) 
to be added as ions. BUT it added the same amount, i.e. 52 Mg ions 
instead of 26 which would be needed for neutralization. The same holds 
for Zn or Ca ions, which also are divalent in ions.itp


Could it be that the routines of genion to determine the number of ions 
are not working properly? I mean, the -neutral option also does work 
only if the -conc flag is also there and provides a value > 0.0 (which 
in fact is not what I want when I just want do neutralize my system by 
adding ions...)


Does anyone of you also had similar problems?

Thank you,
Matthias
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