[gmx-users] Re: PME

Erik Lindahl lindahl at stanford.edu
Tue Jun 18 19:05:12 CEST 2002

Celine Anezo wrote:
> Hi Erik,
> I have a question about the calculation of long range interactions in
> Gromacs using PME. In the energy output file, short range and long range
> contributions to electrostatics are listed for the whole system, but the
> long range contribution doesn't appear for each group separately.
> I have the following problem: I have 12 sugar molecules in a DPPC bilayer
> and I would like to compute the interaction energy between these sugar
> molecules to compare it to the potential energy of the bilayer alone (to
> be sure that interactions between the sugar molecules can be neglected).
> To do this, I need to know the long range term for each group separately.
> Are long range interactions computed for each group separately anywhere?


No - they are not calculated separately for PME, simply because it would 
be extremely expensive to do it. We would have to create a separate grid 
for each group, and then perform PME for all possible combinations of 
grids. With 3 groups we would basically have to do PME 6 times each step!

Now, it MIGHT appear in a future version, but the smartest thing is 
definitely to store your trajectory, rerun mdrun and calculate the 
energies for the stored frames. When you do this you can simply exclude 
all interactions except sugar-sugar.



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