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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> Hi
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