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 - 18:10:48 CDT

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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