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 > 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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