[EMAIL PROTECTED] wrote:
Dear community,
Thanks, Mark! But I can't find any g_energy or log file terms specifically
related to solvent bonded energy (bonds and angles). The log file bonded terms
are for the total system, I guess, but they are very close to the ones I get
when I request their "protein" counterpart from g_energy. My guess would be
that, in my 103-residue protein (1142 at) system solvated by 14'076 water
molecules (42'228 at), there should be a large difference between protein bonded
and solvent bonded terms.
Did you constrain your solvent bonded degrees of freedom to be constant?
Perhaps water bonded terms are not counted at all, as the water molecule
geometry dose not vary with the SPC model, during the simulation?
By the way, is the assumption of my previous mail correct? The one on the total
potential energy formulation as a function of g_energy potential energy
decomposition terms:
Etot = a + 0.5*b + c (+ d), with
a) protein-protein (bonded and non-bonded)
b) protein-solvent (interaction, non-bonded)
c) solvent-solvent (interaction, non-bonded)
(d) solvent bonded terms)
(Of course this only holds when using a non-PME method (i.e. generalised
reaction field) for long range electrostatics!)
Like I said last time, all the non-total and non-kinetic energies must
sum to give the potential energy. There's no reason to go introducing
factors of one-half. There's no purpose in GROMACS reporting a
double-counted protein-solvent interaction.
Mark
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
