Thanks for the help. With your suggestions I was able to center the molecule in the box.<br>Jaya.<br><br><div class="gmail_quote">On Mon, Sep 14, 2009 at 2:57 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">jayalakshmi sridhar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I was under the impression that -box and -d should center the protein in the<br>
solvent box. It says in the manual- Center molecule in box (implied by -box<br>
and -d)<br>
Jaya<br>
</blockquote>
<br></div>
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.<br><font color="#888888">
<br>
Mark<br>
<br>
</font><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
On Mon, Sep 14, 2009 at 2:12 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
jayalakshmi sridhar wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear GROMACS Users,<br>
I am new to GROMACS. I am trying to solvate my protein in a octahedral<br>
box.<br>
I used the following commands after generating the initial .gro and .top<br>
files.<br>
$ editconf -f 1z10_groinit.gro -o 1z10_groinit.gro -box 8.5 -d 0.85 -bt<br>
octahedron<br>
and then<br>
$ genbox -cp 1z10_groinit.gro -cs -o 1z10_groinit_b4em.gro -p<br>
1z10_groinit.top<br>
<br>
But when I visualize the solvated protein in VMD, I see that the protein<br>
is<br>
not centered in the box. All help is greatly appreciated. Thanks.<br>
Jaya.<br>
<br>
</blockquote>
Well you didn't tell it to center on the protein, so the result should be<br>
no particular surprise. Read editconf -h and genbox -h and see what you<br>
learn about how to center things. :-)<br>
<br>
Mark<br>
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