[gmx-users] Re: PME (long range interaction of sugar molecules)

Erik Lindahl lindahl at stanford.edu
Wed Jun 19 19:14:50 CEST 2002

Paul Czodrowski wrote:
> Hi Erik,
> Hi Celine,
>>>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
>>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.
> Can't yout do this via an index.ndx-file?
> In my case, I want to consider the binding affinity of a ligang with a
> protein. When I run grompp & mdrun I use the switch "-n index.ndx" (in
> which I defined the ligand and the protein in 2 different groups, which
> appear at the end of the index.ndx).
> When I run g_energy, I can calculate the interactions between the protein
> and the ligand. Am I doing something wrong?

It doesn't partition the long-range (lattice) part of the energy if you 
use PME, for the reason I described above. The problem is that the PME 
algorithm works with ALL charges at once, not pairs of them.

> By the way: Is there a possibility to consider explicitlz hydrogen bonds?
> Is there any reference, where I can read more, how the interactions are
> being calculated?

Check the references of the forcefields; there used to be a couple of 
forcefields (early versions of Amber for instance) that had explicit 
hydrogen bonds, but all modern forcefields use the normal electrostatic 
interactions to account for hydrogen bonding too.



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