[gmx-users] Implicit solvent
samuel.flores at yale.edu
Sat Mar 26 17:33:17 CET 2005
Thanks for the help on my last question.
I am wondering, what is the status of the implementation of implicit
solvent? I saw a reference to it in the list archives that suggested it was
already implemented. If so, where is it documented?
On Fri, 2005-03-25 at 17:18 -0500, Samuel Flores wrote:
> Howdy all,
> Many thanks for help given in the past.
> I'm currently doing md of a protein in a water box. I'd like to know the
> potential and kinetic energies of the protein alone, the potential energy
> the protein-water interaction. It's my understanding that the g_energy
> Coul-LR:Protein-Protein doesn't exist, because it's included in
> Coul-SR:Protein-Protein for a groupwise energy analysis. So I am to sum
> Coul-SR to Coul-14. But I can't for the life of me find out what exactly
> Coul-14 represents, and why it would not be included in Coul-SR. Can
> enlighten me?
> Also, I would think it would be necessary to include energies due to
> Dihedral bending and Torsion angle twisting in the protein. But, those
> energies are not separated into groups! Am I to assume that all the
> energy is due to the protein? That doesn't seem right -- surely the water
> is responsible for some of that. Also, I don't see a Torsion angle term
> all, even for the system as a whole -- where is this energy?
You probably have no intramolecular energy terms in water, when you're
using settle, shake or lincs.
Torsion == dihedral, so all bonded terms usually come from the protein.
You will have to look for Coul-SR:Protein-Sol etc. If you haven't
defined energy group then you may want to rerun your trajectory. Same if
you have used PME. CHeck archives.
> Thanks in advance for any help you can give.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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