[gmx-users] Does gmx covar/gmx anaeig give <dS> or T<dS> for ligand binding?

[Billy Williams-Noonan]

Hi Gromacs Users,

  I have used gmx covar and gmx anaeig to generate three ensemble average
entropies over 100ns: first for a ligand in solution (<S(L)>), second for a
protein in solution (<S(P)>) and third for their respective complex in
solution (<S(P.L)>).

   My understanding is that the change in entropy upon binding is given by:

<dS> = <S(P.L)> - <S(P)> - <S(L)>   -----------(1)

   Using gmx covar/gmx anaeig I got Quasi-Harmonic entropy estimates of:

<S(P.L)> = 128,886 J/mol/K

<S(P)> = 153,548 J/mol/K

<S(L)> = 4137 J/mol/K

   As stated, these values were generated using gmx covar/anaeig by
selecting for the relevant biomolecule in each ensemble and ignoring the
effect of solvent movement.

   By subbing the above-described values into (1), I got about -28 kJ/mol/K
for <dS>, which is the right answer if the units are actually kJ/mol, and
not kJ/mol/K.  Strangely, upon multiplying by T, I got a value of -8640
kJ/mol, which is quite obviously wrong.

   So does (1) yield a value for <S> or T<dS> ?  Is anyone able to explain
this to me?

   Kind regards,

Billy


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