Hello All
I have used the following ptraj scripts to re-image the trajectories into
the primary simulation box.
trajin traj.mdcrd 1 1000000 20
center :1-125 mass origin
image origin center familiar
trajout traj_reimage.mdcrd
go
I also tried to use "rms first :1-125" and/or "unwrap :1-125" within the
above script. (right before the "center" line)
Good thing is all the waters are retreated back into the primary simulation
box which is the truncated octahedral box. However, the random rotation of
the solute still remains. (The solute is only one big molecule with 125
residues and the solution is just TIP3P water).
Could anybody teach me how to exclue the random rotations here? Any
suggestions would be appreciated.
Thank you very much.
Bin
2011/8/23 Bin Wu <wubin2002.gmail.com>
> Hello Jason
>
> Thank you so much.
>
> So just to be clear. The abrupt change in my trajectory is due to the
> "image" problems and is not becasue of bad simulation results.
> Is that so ?
>
> Thank you again.
>
> Best Regards!
>
> Bin
>
> 2011/8/23 Jason Swails <jason.swails.gmail.com>
>
>> On Tue, Aug 23, 2011 at 6:43 PM, Bin Wu <wubin2002.gmail.com> wrote:
>>
>> > Hello Jason
>> >
>> > Thank you so much for your reply and suggestion. I have attached the MD
>> > info
>> > below. The temperature and density seem normal within the time range
>> when
>> > the abrupt change is observed. But the fluctuation of the pressure and
>> > "VIRIAL" part seem a little bit high. I am not sure whether that kind
>> of
>> > the fluctuation is the normal range.
>> >
>>
>> Pressure fluctuations should be very large since liquid water is largely
>> incompressible. Even small changes to the box volume will give rise to
>> huge
>> fluctuations in pressure. The property you *really* want to look at is
>> the
>> density.
>>
>>
>> >
>> > Please help me take a look.
>> >
>> >
>> > And if it is the imaging problem, I wonder if the below ptraj script
>> could
>> > help me to get rid of it.
>> >
>> > trajin trajin.mdcrd 1 1000000 1
>> > trajout trajout_reim.mdcrd
>> > center :1-125 origin
>> > image origin center
>> > go
>> >
>>
>> It might work. If your main solute has only 1 molecule (residues 1-125),
>> then this will work (don't forget to use "familiar" in your image command
>> if
>> you're using a truncated octahedron). If it has multiple molecules (like
>> for a dimer or a non-covalent receptor-ligand complex), then the two parts
>> of your solute may have imaged separately and the above may not quite push
>> them both back to the same box (and it definitely won't if :1-125 is both
>> molecules). If you have separate solute molecules, you should center and
>> image them 1 at a time to make sure they all get back to the main box.
>>
>> I would also suggest doing an RMS command if the above doesn't get rid of
>> your random rotations.
>>
>> HTH,
>> Jason
>>
>>
>> > Thank you so much for your time and help.
>> >
>> > Bin
>> >
>> >
>> > NSTEP = 91500 TIME(PS) = 433.000 TEMP(K) = 299.28 PRESS =
>> > -153.2
>> >
>> > Etot = -139637.6361 EKtot = 31366.4040 EPtot =
>> > -171004.0401
>> >
>> > BOND = 333.8696 ANGLE = 1219.2331 DIHED =
>> > 888.3422
>> >
>> > 1-4 NB = 393.1022 1-4 EEL = -4878.2346 VDWAALS =
>> > 23170.7455
>> >
>> > EELEC = -192131.0981 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14882.3346 VIRIAL = 16617.3194 VOLUME =
>> > 524560.3318
>> >
>> > Density =
>> > 0.9999
>> >
>> > Ewald error estimate: 0.4968E-05
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 91600 TIME(PS) = 433.200 TEMP(K) = 300.55 PRESS =
>> > -34.1
>> >
>> > Etot = -139507.3879 EKtot = 31499.1734 EPtot =
>> > -171006.5613
>> >
>> > BOND = 349.5890 ANGLE = 1249.4333 DIHED =
>> > 866.8683
>> >
>> > 1-4 NB = 410.9595 1-4 EEL = -4930.6184 VDWAALS =
>> > 23104.5635
>> >
>> > EELEC = -192057.3564 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 15049.8617 VIRIAL = 15436.1087 VOLUME =
>> > 524340.6867
>> >
>> > Density =
>> > 1.0003
>> >
>> > Ewald error estimate: 0.5495E-05
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 91700 TIME(PS) = 433.400 TEMP(K) = 299.40 PRESS =
>> > 122.3
>> >
>> > Etot = -139742.9707 EKtot = 31379.4638 EPtot =
>> > -171122.4345
>> >
>> > BOND = 382.9452 ANGLE = 1249.8666 DIHED =
>> > 849.8379
>> >
>> > 1-4 NB = 403.2674 1-4 EEL = -4886.6380 VDWAALS =
>> > 23463.1125
>> >
>> > EELEC = -192584.8260 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14891.9576 VIRIAL = 13506.1826 VOLUME =
>> > 524588.1851
>> >
>> > Density =
>> > 0.9998
>> >
>> > Ewald error estimate: 0.4682E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 91800 TIME(PS) = 433.600 TEMP(K) = 298.05 PRESS =
>> > 111.2
>> >
>> > Etot = -139911.3187 EKtot = 31237.6344 EPtot =
>> > -171148.9531
>> >
>> > BOND = 407.7906 ANGLE = 1278.7628 DIHED =
>> > 879.4003
>> >
>> > 1-4 NB = 408.6625 1-4 EEL = -4973.8628 VDWAALS =
>> > 23189.2144
>> >
>> > EELEC = -192338.9211 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14758.9807 VIRIAL = 13499.7246 VOLUME =
>> > 524534.1599
>> >
>> > Density =
>> > 0.9999
>> >
>> > Ewald error estimate: 0.5078E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 91900 TIME(PS) = 433.800 TEMP(K) = 300.02 PRESS =
>> > -1.3
>> >
>> > Etot = -139805.5052 EKtot = 31444.3717 EPtot =
>> > -171249.8769
>> >
>> > BOND = 351.4061 ANGLE = 1221.0253 DIHED =
>> > 882.8895
>> >
>> > 1-4 NB = 407.1285 1-4 EEL = -4895.2452 VDWAALS =
>> > 23224.9251
>> >
>> > EELEC = -192442.0061 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14900.9574 VIRIAL = 14915.1173 VOLUME =
>> > 524461.2275
>> >
>> > Density =
>> > 1.0000
>> >
>> > Ewald error estimate: 0.5531E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92000 TIME(PS) = 434.000 TEMP(K) = 300.26 PRESS =
>> > -87.9
>> >
>> > Etot = -139629.1801 EKtot = 31469.2969 EPtot =
>> > -171098.4770
>> >
>> > BOND = 389.1688 ANGLE = 1265.4640 DIHED =
>> > 868.9357
>> >
>> > 1-4 NB = 397.7884 1-4 EEL = -4905.9677 VDWAALS =
>> > 22969.2233
>> >
>> > EELEC = -192083.0894 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14951.2731 VIRIAL = 15946.1196 VOLUME =
>> > 524413.3567
>> >
>> > Density =
>> > 1.0001
>> >
>> > Ewald error estimate: 0.7829E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92100 TIME(PS) = 434.200 TEMP(K) = 300.25 PRESS =
>> > -72.2
>> >
>> > Etot = -139721.5018 EKtot = 31468.0699 EPtot =
>> > -171189.5717
>> >
>> > BOND = 384.1621 ANGLE = 1243.0636 DIHED =
>> > 868.6295
>> >
>> > 1-4 NB = 390.7627 1-4 EEL = -4924.5232 VDWAALS =
>> > 22946.7155
>> >
>> > EELEC = -192098.3818 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14970.8820 VIRIAL = 15789.0527 VOLUME =
>> > 524501.1839
>> >
>> > Density =
>> > 1.0000
>> >
>> > Ewald error estimate: 0.3513E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92200 TIME(PS) = 434.400 TEMP(K) = 298.25 PRESS =
>> > 260.9
>> >
>> > Etot = -139720.8314 EKtot = 31258.7329 EPtot =
>> > -170979.5643
>> >
>> > BOND = 374.7691 ANGLE = 1211.8954 DIHED =
>> > 880.6749
>> >
>> > 1-4 NB = 402.3459 1-4 EEL = -4872.1427 VDWAALS =
>> > 23456.1990
>> >
>> > EELEC = -192433.3057 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14864.0241 VIRIAL = 11909.2750 VOLUME =
>> > 524508.4725
>> >
>> > Density =
>> > 1.0000
>> >
>> > Ewald error estimate: 0.2539E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92300 TIME(PS) = 434.600 TEMP(K) = 300.90 PRESS =
>> > -131.5
>> >
>> > Etot = -139650.3513 EKtot = 31535.9472 EPtot =
>> > -171186.2985
>> >
>> > BOND = 348.0942 ANGLE = 1219.3671 DIHED =
>> > 882.3245
>> >
>> > 1-4 NB = 408.6144 1-4 EEL = -4922.5393 VDWAALS =
>> > 23146.8554
>> >
>> > EELEC = -192269.0148 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14984.5039 VIRIAL = 16473.7450 VOLUME =
>> > 524664.2207
>> >
>> > Density =
>> > 0.9997
>> >
>> > Ewald error estimate: 0.5050E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92400 TIME(PS) = 434.800 TEMP(K) = 299.54 PRESS =
>> > -24.0
>> >
>> > Etot = -139694.6455 EKtot = 31393.5846 EPtot =
>> > -171088.2300
>> >
>> > BOND = 378.8837 ANGLE = 1243.2450 DIHED =
>> > 875.9209
>> >
>> > 1-4 NB = 406.4807 1-4 EEL = -4882.7428 VDWAALS =
>> > 23224.8930
>> >
>> > EELEC = -192334.9104 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14937.4580 VIRIAL = 15209.6861 VOLUME =
>> > 524708.6720
>> >
>> > Density =
>> > 0.9996
>> >
>> > Ewald error estimate: 0.3115E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92500 TIME(PS) = 435.000 TEMP(K) = 300.70 PRESS =
>> > -125.1
>> >
>> > Etot = -139562.8224 EKtot = 31515.0647 EPtot =
>> > -171077.8870
>> >
>> > BOND = 362.7320 ANGLE = 1217.5738 DIHED =
>> > 891.6255
>> >
>> > 1-4 NB = 401.1747 1-4 EEL = -4886.7285 VDWAALS =
>> > 23028.5400
>> >
>> > EELEC = -192092.8046 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14974.9083 VIRIAL = 16392.4614 VOLUME =
>> > 524703.6161
>> >
>> > Density =
>> > 0.9996
>> >
>> > Ewald error estimate: 0.5917E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92600 TIME(PS) = 435.200 TEMP(K) = 297.86 PRESS =
>> > 122.6
>> >
>> > Etot = -139616.4800 EKtot = 31217.5917 EPtot =
>> > -170834.0717
>> >
>> > BOND = 360.5113 ANGLE = 1225.6452 DIHED =
>> > 882.4417
>> >
>> > 1-4 NB = 409.2107 1-4 EEL = -4882.6840 VDWAALS =
>> > 23230.4940
>> >
>> > EELEC = -192059.6906 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14879.5337 VIRIAL = 13491.0475 VOLUME =
>> > 524473.8264
>> >
>> > Density =
>> > 1.0000
>> >
>> > Ewald error estimate: 0.1793E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92700 TIME(PS) = 435.400 TEMP(K) = 300.05 PRESS =
>> > -68.9
>> >
>> > Etot = -139584.9528 EKtot = 31447.5460 EPtot =
>> > -171032.4988
>> >
>> > BOND = 348.0632 ANGLE = 1233.7514 DIHED =
>> > 876.7551
>> >
>> > 1-4 NB = 396.5163 1-4 EEL = -4881.5571 VDWAALS =
>> > 23102.7534
>> >
>> > EELEC = -192108.7812 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14943.5248 VIRIAL = 15723.3403 VOLUME =
>> > 524559.0847
>> >
>> > Density =
>> > 0.9999
>> >
>> > Ewald error estimate: 0.3693E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92800 TIME(PS) = 435.600 TEMP(K) = 299.53 PRESS =
>> > -95.3
>> >
>> > Etot = -139690.7641 EKtot = 31392.7328 EPtot =
>> > -171083.4969
>> >
>> > BOND = 375.6789 ANGLE = 1223.4196 DIHED =
>> > 857.8401
>> >
>> > 1-4 NB = 396.7867 1-4 EEL = -4879.9884 VDWAALS =
>> > 22928.1375
>> >
>> > EELEC = -191985.3714 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14916.9839 VIRIAL = 15996.5476 VOLUME =
>> > 524400.2959
>> >
>> > Density =
>> > 1.0002
>> >
>> > Ewald error estimate: 0.9778E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 92900 TIME(PS) = 435.800 TEMP(K) = 300.46 PRESS =
>> > 34.8
>> >
>> > Etot = -139581.7352 EKtot = 31489.7065 EPtot =
>> > -171071.4417
>> >
>> > BOND = 360.4976 ANGLE = 1209.2194 DIHED =
>> > 862.9193
>> >
>> > 1-4 NB = 403.8898 1-4 EEL = -4915.2626 VDWAALS =
>> > 23036.0507
>> >
>> > EELEC = -192028.7558 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 15002.3521 VIRIAL = 14608.2399 VOLUME =
>> > 524235.7913
>> >
>> > Density =
>> > 1.0005
>> >
>> > Ewald error estimate: 0.3876E-04
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> >
>> > NSTEP = 93000 TIME(PS) = 436.000 TEMP(K) = 299.55 PRESS =
>> > -208.9
>> >
>> > Etot = -139422.9521 EKtot = 31394.9985 EPtot =
>> > -170817.9506
>> >
>> > BOND = 364.7691 ANGLE = 1200.8769 DIHED =
>> > 864.3790
>> >
>> > 1-4 NB = 415.3855 1-4 EEL = -4903.3268 VDWAALS =
>> > 22796.7250
>> >
>> > EELEC = -191556.7592 EHBOND = 0.0000 RESTRAINT =
>> > 0.0000
>> >
>> > EKCMT = 14785.8487 VIRIAL = 17149.7500 VOLUME =
>> > 524179.3503
>> >
>> > Density =
>> > 1.0006
>> >
>> > Ewald error estimate: 0.2604E-04
>> >
>> >
>> > 2011/8/23 Jason Swails <jason.swails.gmail.com>
>> >
>> > > It's a little weird what's happening here. Imaging issues (at least
>> the
>> > > ones I've seen) manifest themselves, typically, as simple translations
>> > (all
>> > > the way to the other side of the periodic box). What I saw from your
>> > > video/animation are abrupt rotations, I think. This could still be an
>> > > imaging issue, especially if you're using a truncated octahedron
>> (since
>> > > there are rotations used in the reimaging process, even though I
>> *think*
>> > > they should be rotated back...).
>> > >
>> > > You should check your energies, densities, and other thermodynamic
>> > > quantities of interest to make sure that you're getting values that
>> make
>> > > sense. If your jumps in your movie are associated with jumps in your
>> > > thermodynamic quantities, then something is messed up. If not (and
>> your
>> > > quantities are behaving nicely), then you likely have some form of
>> > > visualization artifact.
>> > >
>> > > You can delete these by centering and reimaging your system, as well
>> as
>> > > doing an RMS fit of your simulation (which will align all of your
>> frames
>> > to
>> > > eliminate translational/rotational motions).
>> > >
>> > > HTH,
>> > > Jason
>> > >
>> > > On Tue, Aug 23, 2011 at 5:19 PM, Bin Wu <wubin2002.gmail.com> wrote:
>> > >
>> > > > Hello Carlos
>> > > >
>> > > > Thank you very much for your reply.
>> > > >
>> > > > If you have not seen the animation with those links, please check
>> them
>> > > out.
>> > > > It is clear to see them better than I describe.
>> > > >
>> > > > I am using the NPT ensemble. The water molecules are very dispersed
>> so
>> > I
>> > > > cann't really tell whether the dimension of the simulation box
>> changed
>> > or
>> > > > not. But I am sure that the whole simulation system went through
>> > certain
>> > > > sudden deformation within a couple of time steps.
>> > > >
>> > > > As for whether it is the periodic imaging problem, to be honest, I
>> do
>> > not
>> > > > know. That is why turn to this mailing list for help.
>> > > >
>> > > > And of course, I have went through the archive for answer. It is
>> just
>> > > that
>> > > > I
>> > > > have not found simliar cases.
>> > > >
>> > > > Thank you very much.
>> > > >
>> > > > Bin
>> > > >
>> > > >
>> > > >
>> > > > 2011/8/23 Carlos Simmerling <carlos.simmerling.gmail.com>
>> > > >
>> > > > > I don't understand the box twist- are you saying the box
>> dimensions
>> > > > change
>> > > > > in PBC, or your molecule moves?
>> > > > > have you evaluated the energy?
>> > > > > could it be a periodic imaging problem? there is lots of info on
>> this
>> > > in
>> > > > > the
>> > > > > archives. you should use the ptraj image command- but it isn't
>> clear
>> > > > quite
>> > > > > what you want to see, and if you understand how the PBC imaging
>> > works.
>> > > > >
>> > > > >
>> > > > > On Tue, Aug 23, 2011 at 4:53 PM, Bin Wu <wubin2002.gmail.com>
>> wrote:
>> > > > >
>> > > > > > Dear Amber Users
>> > > > > >
>> > > > > > I have observed a very strange phenomenon from trajectory
>> > > visualization
>> > > > > > using VMD. I have attached the GIF format of the trajectory
>> > > animations
>> > > > > > with
>> > > > > > this email. Owing to the fact that this mailing list limits the
>> > size
>> > > of
>> > > > > the
>> > > > > > attachment less than 1024KB, the quality of the GIF is very
>> poor.
>> > > > Movies
>> > > > > of
>> > > > > > higher qualities are listed with the following links:
>> > > > > >
>> > > > > > http://dl.dropbox.com/u/5951953/1.mpg
>> > > > > >
>> > > > > > http://dl.dropbox.com/u/5951953/1.gif
>> > > > > >
>> > > > > > Please check them out.
>> > > > > >
>> > > > > >
>> > > > > > I am simulating a polymer solvated in the truncated octahedral
>> box
>> > > > under
>> > > > > > NPT
>> > > > > > ensemble. The Langenvin dynamics is invoked to control the
>> > > temperature.
>> > > > > The
>> > > > > > input script is actually copied from one official tutorial
>> listed
>> > in
>> > > > > Amber
>> > > > > > Website and is presented below.
>> > > > > >
>> > > > > > polyA-polyT 10-mer: 100ps MD
>> > > > > > &cntrl
>> > > > > > imin = 0, irest = 1, ntx = 7,
>> > > > > > ntb = 2, pres0 = 1.0, ntp = 1,
>> > > > > > taup = 2.0,
>> > > > > > cut = 10, ntr = 0,
>> > > > > > ntc = 2, ntf = 2,
>> > > > > > tempi = 300.0, temp0 = 300.0,
>> > > > > > ntt = 3, gamma_ln = 1.0, ig = -1,
>> > > > > > nstlim = 500000, dt = 0.002,
>> > > > > > ntpr = 100, ntwx = 100, ntwr = 1000
>> > > > > > /
>> > > > > >
>> > > > > >
>> > > > > > The abnormal phenomenon is that the simulation box suddenly
>> changes
>> > > its
>> > > > > > shape like twisting within very short time step intervals. In
>> the
>> > > > movie
>> > > > > > attached, just the solute part is included in order to enable
>> the
>> > > > > audience
>> > > > > > to have a better view. And this kind of twist keeps happening
>> along
>> > > the
>> > > > > > simulation.
>> > > > > >
>> > > > > > In my opinion, the dynamics of the polymer should not be that
>> fast.
>> > > > That
>> > > > > is
>> > > > > > why I think it is very strange. I wonder weather what I saw is
>> > > artifact
>> > > > > and
>> > > > > > if it is could anybody tell me how to get rid of them.
>> > > > > >
>> > > > > > Any comments or suggestions would be highly appreciated.
>> > > > > >
>> > > > > > Thank you very much for your time.
>> > > > > >
>> > > > > > Best Regards!
>> > > > > >
>> > > > > > Bin
>> > > > > >
>> > > > > > _______________________________________________
>> > > > > > AMBER mailing list
>> > > > > > AMBER.ambermd.org
>> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
>> > > > > >
>> > > > > >
>> > > > > _______________________________________________
>> > > > > AMBER mailing list
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>> > > > >
>> > > > _______________________________________________
>> > > > AMBER mailing list
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>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Jason M. Swails
>> > > Quantum Theory Project,
>> > > University of Florida
>> > > Ph.D. Candidate
>> > > 352-392-4032
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Aug 24 2011 - 15:30:02 PDT
