AMBER Archive (2006)

Subject: Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Jun 20 2006 - 19:19:10 CDT

of course my suggestions are just ideas, it is entirely possible
that you have some error. what i meant was that your
observations are not that surprising.

JunJun Liu wrote:

> Dear Dr.Simmerling,
>
> Thanks a lot for the responses. I may not state the problem clearly.
> In this case, GB model is not used. What I did is like the followings:
> 1). MD simulation with explicit solvation box
> 2). extract snapshots from stable MD trajectory and remove waters and
> counterions
> 3). Perform 1 step(single point) gas phase minimization against those
> snapshots
>
> I know the energy from MD simulation contains solvent contribution,
> and this energy should be different with energy from gas phase. But
> it's abnormal that the gas-phase electrostatic energy fluctuate too
> much, which can be up to ~600kcal/mol. This is quite strange! We
> checked the RMSD of selected snapshots, the values are less than
> 0.3A, indicating the selected structures are very close! Any
> suggestions? Thanks!
>
> Regards!
>
> Liu
>
> On Tue, 20 Jun 2006 20:10:48 -0300, Carlos Simmerling
> <carlos_at_csb.sunysb.edu> wrote:
>
>> possible things to consider:
>>
>> 1) the GB solvated system is much smaller, so larger fluctuations
>> are expected (check
>> a stat mech book)
>> 2) you are calculating energies with a different energy function
>> than you used to
>> generate the simulation. It is entirely possible that the energy
>> fluctuations for the
>> trajectory from explicit water differ from what you would get if you
>> used structures
>> that were actually sampled in the GB model.
>> 3) the ele in the explicit water includes solvation, and the GB one
>> does not.
>> it is well known that these terms tend to fluctuate in the opposite
>> direction
>> so leaving the solvation energy out will give higher fluctuations.
>>
>>
>>
>> JunJun Liu wrote:
>>
>>> Hi all,
>>>
>>> It's acutally a sander related problem. The sander program produces
>>> a stable trajectory when performing a MD simulation in explicit
>>> water box, but gives out very unstable energy curve if doing
>>> vacuum single-point energy calculation against snapshots of this
>>> MD trajectory(with waters and counterions removed). What could be
>>> the reason? Since it's a DNA+Protein system, does this mean the
>>> force field(ff99) can't describe the system well? Or caused by
>>> other problem? Any suggestions? Thanks!
>>>
>>> Regards!
>>>
>>> Liu
>>>
>>> On Tue, 20 Jun 2006 10:47:44 -0300, yxiong99 <yxiong99_at_163.com> wrote:
>>>
>>>> Dear sir,
>>>> I have a strange problem when I did MM_PBSA. My system is
>>>> protein-DNA-ligand complex. The receptor is protein-DNA complex,
>>>> and the ligand is a small molecule. I get 50 points from a stable
>>>> 200 ps MD simulation. In that simulation, it is obvious that
>>>> energy for every step in 200ps simulation don't change so much.
>>>> However after I did MM_PBSA(I only did MM section to test), I
>>>> found "ELE " has a large fluctuation.
>>>> Could you please give me some suggestion on it?
>>>> MD results:
>>>> -------------------------------------------------------------------------------------
>>>> A V E R A G E S O V E R 100000 S T E P S
>>>>
>>>> NSTEP = 100000 TIME(PS) = 1200.000 TEMP(K) = 297.94
>>>> PRESS = 1.0
>>>> Etot = -1755294.9287 EKtot = 6319.6873 EPtot =
>>>> -1761614.6160
>>>> BOND = 1374.4608 ANGLE = 5579.4236 DIHED
>>>> = 2833.4301
>>>> 1-4 NB = 2212.7443 1-4 EEL = -5183.5817 VDWAALS
>>>> = -5710.5417
>>>> EELEC = -1762720.5514 EHBOND = 0.0000 RESTRAINT
>>>> = 0.0000
>>>> EKCMT = 1.9203 VIRIAL = -24.2883 VOLUME
>>>> = 1239972.2032
>>>> Density
>>>> = 0.8688
>>>> Ewald error estimate: 0.9679E+00
>>>> ------------------------------------------------------------------------------
>>>> R M S F L U C T U A T I O N S
>>>>
>>>> NSTEP = 100000 TIME(PS) = 1200.000 TEMP(K) = 2.04
>>>> PRESS = 51.9
>>>> Etot = 3.7961 EKtot = 43.3440 EPtot
>>>> = 45.1668
>>>> BOND = 29.6708 ANGLE = 45.6035 DIHED
>>>> = 26.7273
>>>> 1-4 NB = 13.7112 1-4 EEL = 38.6013 VDWAALS
>>>> = 35.0353
>>>> EELEC = 47.8923 EHBOND = 0.0000 RESTRAINT
>>>> = 0.0000
>>>> EKCMT = 0.9180 VIRIAL = 1390.4239 VOLUME
>>>> = 142.3465
>>>> Density
>>>> = 0.0001
>>>> Ewald error estimate: 0.2632E-04
>>>>
>>>> MMPBSA results:
>>>> -------------------------------------------------------------------------------------
>>>> # COMPLEX
>>>> RECEPTOR LIGAND
>>>> # ----------------------- -----------------------
>>>> -----------------------
>>>> # MEAN STD MEAN
>>>> STD MEAN STD
>>>> # ======================= =======================
>>>> =======================
>>>> ELE -23558.26 691.21 -23410.78 683.97
>>>> 61.30 0.02
>>>> VDW -2745.00 28.83 -2730.24 29.06
>>>> 16.89 0.01
>>>> INT 13160.44 52.99 13382.69 54.40
>>>> 54.10 0.04
>>>> GAS -13142.81 696.51 -12758.34 689.12
>>>> 132.29 0.03
>>>> # DELTA
>>>> # -----------------------
>>>> # MEAN STD
>>>> # =======================
>>>> ELE -208.78 64.66
>>>> VDW -31.64 3.68
>>>> INT -276.34 17.50
>>>> GAS -516.77 67.28
>>>>
>>>> 　　　　　　　　Ying Xiong
>>>> 　　　　　　　　yxiong99_at_163.com
>>>> 　　　　　　　　　　2006-06-19
>>>>
>>>
>>>
>>>
>>
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