[gmx-users] protein not centered in solvent box
Mark.Abraham at anu.edu.au
Mon Sep 14 21:57:33 CEST 2009
jayalakshmi sridhar wrote:
> I was under the impression that -box and -d should center the protein in the
> solvent box. It says in the manual- Center molecule in box (implied by -box
> and -d)
Yes, but they aren't meant to work in concert. Specifying both the size
of the box and the distance between the solute and the edges of the box
is only uniquely defined for a very lucky solute.
> On Mon, Sep 14, 2009 at 2:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>> jayalakshmi sridhar wrote:
>>> Dear GROMACS Users,
>>> I am new to GROMACS. I am trying to solvate my protein in a octahedral
>>> 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
>>> 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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