[gmx-users] Placing ions at a required distance

[shivangi nangia]

Thanks, I did it manually using 'cat'.
Thanks for your time.

-Shivangi

On Mon, Mar 28, 2011 at 4:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> shivangi nangia wrote:
>
>> Hi again,
>>
>> I did not quite understand the suggestion.
>> I have successfully added Li+ ions in my simulation box using genion.
>> I am confused about how to place Li+ ions using editconf.
>>
>>
> Are these ions simply going to be part of the bulk solution?  If so, use
> genion.  Manual intervention is not necessary since random initial
> velocities will disrupt any sort of idealized geometry that you construct.
>
>
>  Will I have to create a .gro and .itp file and add it like a solute ?
>>
>>
> Yes and no.  If you really believe you need a specific location of a Li+
> ion in your simulation cell, either (1) write a simple .gro file by hand and
> concatenate it with the coordinate file of your other system components or
> (2) use editconf -center to define its coordinates and concatenate that file
> with your system.  Li+ parameters should be present in ions.itp for most
> force fields, so just #include that topology like you would any other
> system.
>
> -Justin
>
>  Thanks,
>> Shivangi
>>
>>
>>
>>
>> On Mon, Mar 28, 2011 at 3:26 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    shivangi nangia wrote:
>>
>>        Hello,
>>
>>        I am a new gromacs user.
>>
>>        I want to place Li+ ions at a required distance from the
>>        polypeptide ( which is at the centre of a box of water)
>>
>>        I searched through the archive and the manual if there is a
>>        way/provision to do this, but could not.
>>
>>        Is there a way?
>>
>>
>>    Measure the distance you want and establish the coordinate at which
>>    you wish to place the ion, then use editconf -center to place it at
>>    the proper location in the simulation box.
>>
>>    -Justin
>>
>>
>>
>>        Please guide.
>>
>>        Thanks,
>>        Shivangi
>>
>>
>>
>>
>>    --     ========================================
>>
>>    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
>>    <tel:%28540%29%20231-9080>
>>
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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