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

[Justin A. Lemkul]

rasoul nasiri wrote:
> 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?

Why bother adding solvent if you're just going to remove it?  Here's what I 
would do:

1. Position solutes in the box with editconf -center
2. Add co-solvents (with a large value of -vdwd, I suppose)
3. Add solvent

I don't fully grasp why the initial position of the co-solvents matters so 
precisely; you may have a hard time satisfying all of the simultaneous distance 
requirements.  Everything is just going to diffuse around anyway during MD. 
Maybe you have some reason I'm not thinking of, but it's a potentially 
complicated problem to build.

-Justin

> 
> Rasoul
> 
> On Sat, Apr 17, 2010 at 5:43 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 <http://vt.edu> | (540) 231-9080
>     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

========================================