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

Paul Czodrowski pc at rufus.biomed.brown.edu
Wed Jun 19 18:52:21 CEST 2002

Hi Erik,
Hi Celine,

>> Are long range interactions computed for each group separately

> Hi,
> 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.

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
being calculated?
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. :)



Paul Czodrowski

Department of Molecular Pharmacology
Biomedical Center
Box G-B4, Brown University
Providence, Rhode Island 02912 USA
voice: +1 401 863 9841

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