[gmx-users] How can I maintain a distance of at least 0.5 nm from each other of solutes

[rasoul nasiri]

Hi,
Thanks for the replies.
Since I want to increase distance among co-solvents with themselves and with
solutes, i must firstly fill the co-solvents along solutes and solvents
after that i remove solvent, finally by edittconf -translate the co-solvents
uniformally is distributed in the appropriate distances. Is it OK?

Rasoul

On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Justin A. Lemkul wrote:
>
>
>>
>> rasoul nasiri wrote:
>>
>>> Dear Justin,
>>> Hello again
>>>
>>> Thanks for the message. I want to increase the distance between solutes
>>> in simulation box before MD simulation. How can I do it?
>>>
>>>
>> You can't.  If you know you need a certain distance, that should be part
>> of your planning :)  I suppose you could run a pulling simulation to
>> separate your two species, but that requires substantially more work (and
>> setup considerations) than the two or three quick editconf commands to
>> properly build the system.
>>
>>
> Correction: you can use editconf -translate with appropriate index groups
> to separate your solutes.  This will also imply that you haven't added
> solvent, which is the same thing as positioning the two solutes
> appropriately in the first place (with editconf -center, as I posted
> before).
>
> -Justin
>
>
> --
> ========================================
>
> 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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