[gmx-users] protein comes out of the box

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Feb 25 02:11:01 CET 2004

>      I am stimulation an unfolded protein in vaccum. i have the problem that
>my protein is going completely outd side of the box after 20 ps. only small
>tail is inside the box.

Nothing to worry about, as if you have PBC enabled then the chain that 
visually appears to be outside the box is actually entering the box on the 
opposite side.  The molecules are kept whole in the files, even though 
sections of it are actually sticking in the opposite side of the box.

You can use editconf or trajconv to place move the center of the box so 
that it is where the molecule is.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.

More information about the gromacs.org_gmx-users mailing list