[gmx-users] protein not centered in solvent box
Mark.Abraham at anu.edu.au
Mon Sep 14 21:12:11 CEST 2009
jayalakshmi sridhar wrote:
> Dear GROMACS Users,
> I am new to GROMACS. I am trying to solvate my protein in a octahedral box.
> I used the following commands after generating the initial .gro and .top
> $ editconf -f 1z10_groinit.gro -o 1z10_groinit.gro -box 8.5 -d 0.85 -bt
> and then
> $ genbox -cp 1z10_groinit.gro -cs -o 1z10_groinit_b4em.gro -p
> But when I visualize the solvated protein in VMD, I see that the protein is
> not centered in the box. All help is greatly appreciated. Thanks.
Well you didn't tell it to center on the protein, so the result should
be no particular surprise. Read editconf -h and genbox -h and see what
you learn about how to center things. :-)
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