[gmx-users] comparing gmx GB energy with Amber11

[Sandeep Somani]

Hi Per

Pls see inline comments:


> 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.
>

Yes, gromacs prints out "GB Polarization" and "Nonpolar Sol."
corresponding to "EGB" and "ESURF", respectively, from Amber.
Right now I am just comparing EGB part (non polar also do not match but
since it is a much smaller contribution, will worry about that later!).



>
> 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)
>

Just tried -- no change.
(btw, i didnt know 0 => no-cutoff. thnx!)


>
> 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.
>
> I'll try shortly.


> 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?
>
> I tried both "set default PBradii mbondi" and "set default PBradii
mbondi2" while creating amber prmtop files in leap. The difference in EGB
is just 2-3 kcal/mol .. not enough to bridge the gap.

Best
Sandeep







> 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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Hi