[gmx-users] Centering the system

[Shima Arasteh]

I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee?


Thanks a lot.



Sincerely,
Shima



On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:




On 10/16/13 8:29 AM, Shima Arasteh wrote:
>
>
> Dear gmx users,
>
> I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of the x-y plane of the bilayer. I' d like to know if there is any way to use the properties of the pbc and see the peptide in center of the x-y  plane while interacting with the polar groups?
>

trjconv has a number of ways to deal with this.  Please read trjconv -h.

-Justin

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Justin A. Lemkul, Ph.D.
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