[gmx-users] Re: PME (long range interaction of sugar molecules)
pc at rufus.biomed.brown.edu
Wed Jun 19 18:52:21 CEST 2002
>> Are long range interactions computed for each group separately
> 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?
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
How do other peoplo quantify binding affinities? Do you need to run a
thermodynamic for evaluating the free energis?
Oh, these were more questions than answers. :)
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