[gmx-users] Different coulomb energies of protein by Cut-off and PME

[Anton Feenstra]

Zhiyong Zhang wrote:

> Dear gmx users,
> 
> For the same protein, I performed a MD simulation using Cut-off and PME,
> respectively. The following are parameters:
> 
> For Cut-off:
[...]
> rlist                    = 1.0

> 
> For PME:
[...]
> rlist                    = 0.9

> Cut-off:
[...]
> Coul-SR:Protein-Protein     -8733.4    314.267    287.225 -0.0883592  

> 
> PME:
[...]
> Coul-SR:Protein-Protein    -1314.89    79.1684    75.3171 -0.0140827  

> 
> I noticed that, the total coulomb energies in the protein by Cut-off and
> PME are quite different. Would you please explain it? Thanks!

As you can see above, your short-range cutoff (i.e., rlist) is different 
for 'cutoff' and 'pme'. That makes a difference of a factor of 
(0.9/1.0)^3 ~ 0.7 in short-range interactions in the protein. The 
difference does seem larger than this would account for, though.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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