[gmx-users] Implicit solvent

[Samuel Flores]

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?

Sam

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
of
> the protein-water interaction.  It's my understanding that the g_energy
term
> 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
anyone
> 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
bending
> 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
at
> 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.
> 
> Sam    
> 
> 
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-- 
David.
________________________________________________________________________
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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