[gmx-users] jump peptide

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 11 13:32:33 CET 2008

shahrbanoo karbalaee wrote:
> Dear Justin/Mark
> hi
> I have a system with peptide and tfe/spc .I minimized and run for
> equilbrate them for 5 ns.when the pr-md was end the time.I saw  the
> gromac file  by vmd.the peptide jump from the box .but when I saw ngmx
> and choose triclinic ,the peptide was insert in box.I have chosen - bt
>  dodecahedron  in my commands.please advise me.

Read about periodic boundary conditions.


> best


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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