[gmx-users] increasing cut-off and PME grid spacing
jiangsl at phys.sinica.edu.tw
Sun Aug 21 08:25:31 CEST 2011
I understand now.
The vector of box changed from 5.8 to 44 after the short MD for equilibrium.
I don't know what happened during equilibrium.
But that is belong to the other question now.
Thank you very much for your reply.
> Hsin-Lin Chiang wrote:
> > Hi, Justin
> > Sorry for the unclear message.
> > My box vector in .gro file are 44.22834  44.22834  44.22834 and the
> > number of atoms is 20171
> You've set an unreasonably large box, as I expected.  The box should be set in
> nm, not Angstrom.  20171 atoms is a fairly small system, and in effect what
> you've created is a protein in a droplet of water, surrounded by vacuum.  90% of
> the work done by PME will be to calculate a grid of nothing.
> > The output of grompp is shown below,
> > I don't know if it is enough and I'm sorry I don't know how should I do
> > after you reply.
> > Could you please give me more messages in detail?
> The solution is to set a correct box, unless your objective is to simulate a
> droplet, in which case you have no choice but to take the performance loss
> inherent to using PME.
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