Stefano Meliga wrote:
Hi gmx users,
I defined an octahedral box with this line:
$grxdir/editconf -f 1AKEallH.gro -o 1AKEallHbox.gro -bt octahedron -d 0.6
and then I solvated my protein with SPC water model:
$grxdir/genbox -cp 1AKEallHbox.gro -p 1AKEallH.top -o 1AKEallHsol.gro -cs
I am now watching the trajectory of an MD simulation with a molecular
visualisation software (VMD) and I noticed 2 unexpected things:
1) part of the molecule is outside the box
2) the box is cubic
Although the molecule is out of the box, the periodic boundary
conditions should ensure a correct behaviour, still, why is it cubic?
Right, because in a periodic system, there is no "outside," nor are there edges.
The cubic appearance of the box is simply a visualization issue. You can
retrieve your true box shape by using trjconv -pbc mol -ur compact.
-Justin
Note: after solvation, the system was neutralised with genion, then an
EM steep, an EM cg and a all-bonds constrained MD were performed
before the actual MD.
Any ideas?
Thanks,
Stefano
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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