Re: [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 <jalem...@vt.edu 
<mailto:jalem...@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

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