[gmx-users] comparing gmx GB energy with Amber11
Sandeep Somani
ssomani at gmail.com
Fri Nov 9 20:56:49 CET 2012
Just to add to that -
The non-polar term of GBSA do not match between gmx and Amber11, presumably
due to different algorithms for computing the surface area.
I tried the different surface area options (gbsa keyword) in Amber11, but
it didn't help.
fyi.
Best
Sandeep
On Fri, Nov 9, 2012 at 8:32 AM, Per Larsson <per.larsson at sbc.su.se> wrote:
> After some investigation, it turns out that this is explained by the
> differences in input radii for the GB-calculation done by Gromacs and Amber.
> The radii in the gbsa.itp-file are not the same as the ones used by Amber.
>
> If one changes the radii in gbsa.itp, you get a difference in 0-step
> energy (at least for the system below) of 0.2 kJ/mol, which is tolerable. I
> have pasted a copy of the gbsa.itp-file below, in case it is useful for
> someone. This was tested with amber99sb.
>
> Cheers
> /Per
>
> [ implicit_genborn_params ]
>
> ; atype sar st pi gbr hct
> ;Br 0.1 1 1 0.125 0.85 ; H
> C 0.172 1 1.554 0.17 0.72 ; C
> CA 0.18 1 1.037 0.17 0.72 ; C
> CB 0.172 0.012 1.554 0.17 0.72 ; C
> CC 0.172 1 1.554 0.17 0.72 ; C
> CN 0.172 0.012 1.554 0.17 0.72 ; C
> CR 0.18 1 1.073 0.17 0.72 ; C
> CT 0.18 1 1.276 0.17 0.72 ; C
> CV 0.18 1 1.073 0.17 0.72 ; C
> CW 0.18 1 1.073 0.17 0.72 ; C
> C* 0.172 0.012 1.554 0.17 0.72 ; C
> H 0.1 1 1 0.13 0.85 ; H
> HC 0.1 1 1 0.12 0.85 ; H
> H1 0.1 1 1 0.12 0.85 ; H
> HA 0.1 1 1 0.12 0.85 ; H
> H4 0.1 1 1 0.12 0.85 ; H
> H5 0.1 1 1 0.12 0.85 ; H
> HO 0.1 1 1 0.12 0.85 ; H
> HS 0.1 1 1 0.12 0.85 ; H
> HP 0.1 1 1 0.12 0.85 ; H
> N 0.155 1 1.028 0.155 0.79 ; N
> NA 0.155 1 1.028 0.155 0.79 ; N
> NB 0.155 1 1.215 0.155 0.79 ; N
> N2 0.16 1 1.215 0.155 0.79 ; N
> N3 0.16 1 1.215 0.155 0.79 ; N
> O 0.15 1 0.926 0.15 0.85 ; O
> OH 0.152 1 1.080 0.15 0.85 ; O
> O2 0.17 1 0.922 0.15 0.85 ; O
> S 0.18 1 1.121 0.18 0.96 ; S
> SH 0.18 1 1.121 0.18 0.96 ; S
>
> ; masscenters for vsites do not have gbsa parameters
>
> MNH3 0 0 0 0 0
> MCH3 0 0 0 0 0
>
>
>
> 8 nov 2012 kl. 23:42 skrev 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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