Hi peter I think the important is to don't couple small number of atoms(ligand molecules or a few ions) separately to a reference tempreture! It probably will result the same if you make two tcouple groups as below: Protein-LIG water-ions or Protein water-ions-LIG
I think they will be equvalent( with a good approximation)! On Mon, Apr 11, 2011 at 10:32 AM, Peter C. Lai <p...@uab.edu> wrote: > Any rationale behind the thermostat coupling of a ligand with the protein > instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme > binding example)? Especially with small drug-type molecules as generally > the > ligand might/would take the usual place of solvent within a binding region > or other solvent accessible surface and it might be more realistic to > simulate the ligand as part of the solvent's ensemble (one might run two > simulations in order to compare the ligand-protein interaction to the > water-protein interaction at the interaction interface...) > > -- > =============================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | BEC 257 > Genetics, Div. of Research | 1150 10th Avenue South > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > =============================================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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