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On 1/12/2011 10:24 AM, mu xiaojia wrote:
<blockquote
cite="mid:CABSFTFq5GE=4FJXaOb6-_hk8cjZ7rN=Ha1taANLKoyujme-sDQ@mail.gmail.com"
type="cite">
<div class="gmail_quote">Dear gmx-users,
<div><br>
</div>
<div>I want to make a long nano-fiber composed of many
non-covalently bonded proteins, it elongates along the Z
axial direction.<br>
<div><br>
</div>
<div>in editconf, we can define the "Distance between the
solute and the box", but it works for x,y and z directions
at the same time.</div>
<div><br>
</div>
<div>e.g. my command </div>
<div>editconf -f protein.gro -o protein_box.gro -c -d 1.0 -bt
cubic, then the out come would be a box with of at least
1.0 nm "<span style="font-family:Arial">between any two
periodic images of a protein</span>".</div>
<div><br>
</div>
<div>What should I do if I want to set the distance for z axis
smaller than x and y? which means, let the molecules along Z
"see" each other within 2nm? </div>
</div>
<br>
</div>
</blockquote>
<br>
Observe the box created by -d 1.0 and then start again with editconf
-box and choose dimensions you want.<br>
<br>
Mark<br>
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