[gmx-users] increasing cut-off and PME grid spacing

Hsin-Lin Chiang jiangsl at phys.sinica.edu.tw
Sun Aug 21 08:25:31 CEST 2011

Hi Justin,

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.

Sincerely yours,
> 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. 
> -Justin

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