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

[David van der Spoel]

On 17/06/15 20:48, Fabian Thielemann wrote:
> 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.
Forget it. It is so innacurate as to be useless.
The method was published in nature of course.
>
> 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


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se