[gmx-users] Problem in calculating solvation free energy estimates with gmx sasa -odg

[Fabian Thielemann]

Hello everyone,

I want to calculate estimates for the solvation free energy using gmx 
sasa -odg from gromacs-5.0.4 . I applied it in the same way to two 
different types of trajectories. I used gromacs-4.5.6 and the same mdp 
file for all simulations, the only difference being structure and 
forcefield/water model.

The first type of trajectories was of Alanine Dipeptide at different 
temperatures performed in a NVT ensemble using AMBER99SB-ILDN as a 
forcefield and TIP3P as water model. In these cases I got regular output.
The second type are trajectories of Trialanine with different 
protonation states, performed in a NVT ensemble using OPLS-AA as 
forcefield (due to lacking support of differing protonation states in 
AMBER) and TIP4P as water model. In this case, using gmx sasa -odg 
results in a timerow of constant value 0, although the output in 
area.xvg seems to be okay. This was independent of the termini 
protonation (i.e. also for standard termini).

I was neither able to find an explanation to this behaviour in the 
manual for gmx sasa nor in the paper that was referenced for the 
calculation of solvation energies(Eisenberg and McLachlan(1986)).
What exactly does gmx sasa evaluate in this case? What might I have 
missed here? If needed, I can send additional information 
(mdp/conf/area.xvg/dgsolv.xvg).

 From the referenced paper (Eisenberg and McLachlan(1986)), I concluded 
that I could also calculate the solvation free energy from the solvent 
accessible surface of every atom type and the respective atomic 
solvation parameters (ASP). For comparability i would like to know: does 
gmx sasa use the ASP values from this paper or does it use other ASP 
values, for example taken from later publications of Eisenberg?

Thanks in advance!

Fabian