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On 21/03/2011 11:29 AM, Moeed wrote:
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cite="mid:AANLkTikz0K1yDqekPjKiCJs0Oobx8EYVRYR2WvxvdMBH@mail.gmail.com"
type="cite">It is likely that you can use genconf to replicate a
single hexane in a small box (using editconf) to get something
close to the right density and size. This will have more hexane
molecules in it, because some will be removed when you use this
box to solvate the PE later. Equilibrate this box for a while.<br>
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<div> Thank you Justin and Mark for suggestions.<br>
<br>
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Take your straight-chain PE and simulate it in vacuo for a
bit until you get a reasonable-looking non-extended
conformation that will fit in your intended box size. Use
editconf to put your desired box around that.<br>
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Is it not simpler if I take this PE in the right box size
(editconf) and use <br>
<br>
<i><span>genbox -cp </span></i> non-extended-PE in vacuo<i><span>.gro
-ci
Hexane.gro -o -nmol 110 </span></i><br>
<br>
so that I have exact number of solvet. (so no need to worry
about removal of some hexane after insertion PE when using
command below:)<br>
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<br>
No, because genbox -ci does not achieve the kind of close-packing
that will result in the correct density. It inserts molecules in
random interstices - i.e. anywhere. In general, that will not
achieve the close-packing consistent with condensed fluids. genconf
allows you to get closer to this objective by choosing a box to
tessellate, but then you have to equilibrate for a while to de-order
the system.<br>
<br>
It might be possible to get the right number of insertions into your
box if you allow too much volume and then do gentle compression, but
the presence of voids will make the system hard to keep stable, as
you've learned. A couple of goes at genconf will be faster than
that, even if compressing works.<br>
<br>
Mark<br>
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