[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:
> 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.

-Justin

> Rasoul
> 
> On Sat, Apr 17, 2010 at 5:16 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     rasoul nasiri wrote:
> 
>         Dear All,
>         Hello
> 
>         I understand one can adjust distance of between solvent
>         molecules by genbox command and -vdwd  but I don't know, how do
>         it between the solutes?
> 
> 
>     Position your solutes using editconf -center, then add solvent.
> 
>     -Justin
> 
>         Thanks for helping!
> 
>         Rasoul
> 
> 
>     -- 
>     ========================================
> 
>     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

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