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

[Justin A. Lemkul]

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

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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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