Hi
A few things:
1. If I recall correctly, the GB-energy in gromacs is split into two parts,
GB-polarization and non-polar solvation. Can you check whether this is the case
and if the value you report is the sum of those two terms.
2. Try setting all cut-offs to 0 (infinite cutoffs). That will trigger a
slightly different part of the code to do the GB-calculation (you should see in
your log file references to all-vs-all kernels)
3. Try running in single precision, keeping in mind 1 and 2 above to see if
that helps. Also, try setting the GMX_NOOPTIMIZEDKERNELS variable to 1 (at
least it used to be called that, someone else can perhaps correct me if that
has changed). This will make the code run without the sse-loops.
4. It could be that you are using different radii for the atoms in your system.
For amber, are you using the Bondi-radii or something else?
Cheers
/Per
8 nov 2012 kl. 05:43 skrev Sandeep Somani:
> Hi,
>
> I am comparing single point amber ff energies from gmx4.5.5 (double
> precision) and Amber11.
>
> All bonded and non-bonded energy terms are in very good agreement (within
> 0.1 kJ/mol) except GB:
> gmx 'GB polarization' = -200 kJ/mol
> amber 11 'EGB' = -283 kJ/mol.
>
> I am basically trying to replicate Amber's "igb=5 + large cutoff" in gmx.
> According to Amber manual igb=5 corresponds to "model 2 of [2004 OBC
> paper]".
>
> I translated this to the following mdp options:
> ----
> implicit_solvent = GBSA
> gb_algorithm = OBC
> All cut-offs (rcoulomb, rvdw, rlist, rgbradii) larger than the size of the
> molecule.
> {gb_epsilon_solvent, gb_saltconc, gb_obc_alpha, gb_obc_beta, gb_obc_gamma,
> gb_dielectric_offset} = corresponding Amber input.
> ----
>
> Is that correct?
>
> I realize that this is as much a question for Amber mailing list, but
> trying here first! Any idea?
>
> The molecule is ala-12. I'll be happy to send input files.
>
> Thanks in advance
>
> Sandeep
>
> --
> Postdoc
> Wales Group
> Cambridge
> --
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