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<font size="2"><b></b>Hi Justin,
<br />
<br />I understand now.
<br />The vector of box changed from 5.8 to 44 after the short MD for equilibrium.
<br />I don't know what happened during equilibrium.
<br />But that is belong to the other question now.
<br />Thank you very much for your reply.
<br />
<br />Sincerely yours,
<br />Hsin-LIn
<br />>
Hsin-Lin Chiang wrote:
<br />>
> Hi, Justin
<br />>
>
<br />>
> Sorry for the unclear message.
<br />>
> My box vector in .gro file are 44.22834  44.22834  44.22834 and
the
<br />>
> number of atoms is 20171
<br />>
<br />>
You've set an unreasonably large box, as I expected.  The box should be set
in
<br />>
nm, not Angstrom.  20171 atoms is a fairly small system, and in effect what
<br />>
you've created is a protein in a droplet of water, surrounded by vacuum.  
90% of
<br />>
the work done by PME will be to calculate a grid of nothing.
<br />>
<br />>
> The output of grompp is shown below,
<br />>
> I don't know if it is enough and I'm sorry I don't know how should I do
<br />>
> after you reply.
<br />>
> Could you please give me more messages in detail?
<br />>
<br />>
The solution is to set a correct box, unless your objective is to simulate a
<br />>
droplet, in which case you have no choice but to take the performance loss
<br />>
inherent to using PME.
<br />>
<br />>
-Justin
<br />
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