[gmx-users] comparing gmx GB energy with Amber11
Per Larsson
per.larsson at sbc.su.se
Fri Nov 9 14:32:20 CET 2012
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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