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.
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
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
> > > 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
> _______________________________________________
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Received on Tue Aug 23 2011 - 16:00:02 PDT
