[gmx-users] comparing gmx GB energy with Amber11

[Sandeep Somani]

Hi Per

I tried with single precision gmx as well. No change.

Will send you input files soon.

Best
Sandeep

On Thu, Nov 8, 2012 at 3:55 PM, Per Larsson <per.larsson at sbc.su.se> wrote:

> Hi
>
> Thanks for doing those test. They are all reassuring, I think.
> Could you maybe send me your input-files off list and I'll take a look.
> I suspect the issue is that different radii are being used, as Gromacs
> does not use the Bondi radii.
>
> Cheers
> /Per
>
>
> 8 nov 2012 kl. 16:35 skrev 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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