[gmx-users] Flexible SPC and protein potential energy contributions

pascal.baillod at epfl.ch pascal.baillod at epfl.ch
Thu Aug 16 22:05:43 CEST 2007

Dear community,

Thanks again, Mark! Your comments made me realize that I was mixing two concepts
and allowed me to figure out what was going on. I apologize for the confusion.
The correct formulations are:

a) protein-protein (bonded and non-bonded)
b) protein-solvent (interaction, non-bonded)
c) solvent-solvent (interaction, non-bonded)
(d) solvent bonded terms)

E_pot_tot = a + b + c (+ d) [WITH NO 0.5 FACTOR]


E_pot_prot = a + 0.5*b 

...where E_pot_prot would define the potential energy of a protein subsystem,
including all protein bonded terms, all protein to protein interactions, as well
as all solvent to protein (and not protein to solvent, therefore the term *0.5).

In order to cross-check this formulation, I was summing up potential energy

Although I use SHAKE constraints to describe bonds and angles, my SPC water is
rigid, since I have not set "defines" to "-DFLEXIBLE" in my input file. So it IS
normal that I obtain the same values for bonded potential energy terms in the
log file and from g_energy uppon request of protein terms. I guess rigid SPC
bonding energy terms, which would never vary, are simply not counted in the
total potential energy. In my case, "d" is thus equal to 0. 

But the "RF excl." term (removing RF correction for "1-4" electrostatic
interactions and other excluded pairs) also has to be added in order to get the
final sum correct. If I call this term "e", we get:

E_pot_tot = a + b + c + e

Dose anybody know if this last term, "RF excl", is computed / written separately
for protein / water atoms? I would be interested in the "RF excl" contributions
coming from protein atoms only.. Are there such terms for intra-molecular water
to water atom interactions also, or are they limited to the "1-4" interactions
of the protein? In the first case, I guess they would not be counted anyway,
with my rigid SPC water?

Thanks for any feedback!


Pascal Baillod (PhD student) 
Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
CH-1015 Lausanne	

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