From: Charles Danko (dankoc_at_gmail.com)
Date: Tue Dec 14 2004 - 13:31:21 CST
Once again, good response!
I have tried running under an NPT ensemble and gotten an error about
the unit volume becoming too small. I haven't tried this since a real
NVT equilibration, however; I will start a run now with the output of
the 2ns equilibration and post the result.
I thought it interesting what Brian said about the trend toward
decreasing VDW energies. You are, of course, correct based on what I
posted. It is not clear to me if it is a general trend, however (I
posted energies taken from an earlier timepoint below, which have a
lower VDW energy). Is there a software package (or a just a perl
script) which will parse the output files into a TSV file, or
something that I can use to make a graph?
Thanks again for all of your help!
Charles
WRITING COORDINATES TO DCD FILE AT STEP 1665000
ENERGY: 1665000 18329.5908 21638.8262 6834.5290 306.9478
-149897.1544 4037.7323 0.0000 0.0000 51929.8566
-46819.6717 299.8645 -46184.4928 -46176.2742 300.1418
457.4945 -383.1732 763614.3676 -240.3497 -240.8629
ENERGY: 1666000 18140.3738 21481.5798 6871.6239 311.5873
-149563.9700 4274.5122 0.0000 0.0000 51879.4034
-46604.8895 299.5732 -45963.0860 -45981.3652 300.4827
1053.0229 45.8545 763614.3676 -235.7364 -235.8333
On Tue, 14 Dec 2004 09:45:13 -0800 (PST), Brian Bennion
<brian_at_youkai.llnl.gov> wrote:
> Thank you for the comments.
>
> The low pressure is a result of the VDW contacts working themselves out.
> In most of the energy entries in the log file that was posted, the VDW
> energy was getting smaller (approaching negative values) and the pressure
> was decreasing. Hence my brief/terse/short response based on the info
> given.
>
> Technically, not physically speaking, the magnitude of the shrinkage may
> precipitate other problems in regards to patch/grid size where patches become
> unpopulated and NAMD becomes unhappy, as does the user.
>
> There have been other postings where no major pathologies were present
> during minimization and sometimes after equilibration, but production runs
> ran afoul various errors.
>
> Regards
> Brian
>
>
> On Mon, 13 Dec 2004 nordgren_at_sas.upenn.edu wrote:
>
> > Hello all:
> >
> > Brian, you always have sage advice to share on this list... but I think in
> > this case I may disagree with your brief analysis. The thing is, Charles'
> > total system energy is negative and quite large (compared to the VdW
> > component), due to the (large, negative) electrostatic interactions. In
> > such a situation, a net positive VdW energy (especially when it is still
> > smaller than the bonded energy components, i.e.,
> > bonds/angles/torsions)doesn't really surprise me. If the initial conditions
> > had close-contacts that were not removed by minimization, then the system
> > would either fall apart early on, or (as appears to be the case here) they
> > would be removed over the course of 2 million steps of dynamics. (Of
> > course, it's *possible* that some pathological topology exists somewhere in
> > the system, allowing some high-energy close-contacts to be trapped and
> > persist for nanoseconds... I guess it couldn't hurt to check for that.)
> >
> > Carlos, thanks for those links -- the second one is a particularly good
> > read. All I would add is a reminder that the "PRESSURE" and "GPRESSURE"
> > columns are not particularly interesting, since they represent instantaneous
> > values; moreover, if one is using multiple timestepping (evaluating the
> > nonbonded forces only, say, every other timestep) then you can get a *very*
> > misleading idea of what is going on, because the pressure values you see
> > reported are only for timesteps when the nonbonded forces aren't included.
> > What one needs to look at, instead, is the average pressure (i.e., PRESSAVG
> > or GPRESSAVG).
> >
> > So Charles, given the above, it looks like your system is sitting in a
> > situation of slight under-pressure (about -150 bars or so), which for an NVT
> > liquid simulation is also not so surprising -- this would result from a
> > system volume that is just ever so slightly too large (again, see Carlos'
> > second link).
> >
> > As for whether/how the results of an MD simulation are affected by running
> > in
> > an under-pressure NVT ensemble, this is a more detailed question, that
> > requires consulting the journal literature....
> >
> > Hope this is helpful for now!
> >
> > -Erik
> >
> > C. Erik Nordgren, Ph.D.
> > Department of Chemistry
> > University of Pennsylvania
> >
> >
> > Quoting Brian Bennion <brian_at_youkai.llnl.gov>:
> > >
> > > hi charles,
> > >
> > > it would appear that the system is NOT equilibrated. A brief look at
> > > your
> > > VDW energies suggests that there is still some room to minimize poor
> > > interations. That value should not be positive.
> > > Have you minimized by component? what were the gradient values after
> > > minimization of the complete system?
> > >
> > > Regards
> > > Brian
> >
> >
> > Quoting "carlos n. a." <carlosjavierna_at_hotmail.com>:
> > > Hi. maybe you can read this
> > >
> > > http://amber.scripps.edu/Questions/mail/32.html
> > > http://amber.scripps.edu/Questions/pressure.html
> >
> >
> > > On Mon, 13 Dec 2004, Charles Danko wrote:
> > Dear community,
> >
> > Pasted below are a sample of my output energies. I am concerned by
> > the pressure readings. I have read in a previous thread that it is
> > normal for the pressure to jump around a lot (I am using an NVT
> > ensemble), but these values seem rather excessive to me, since I used
> > a water and lipid box which (I believe) was equilibarated to 1bar.
> > Would anyone give me feedback on whether they think that these
> > pressures negatively affect my simulation?
> >
> > Thanks in advance!!
> > Best wishes,
> > Charles
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2149000
> > ETITLE: TS BOND ANGLE DIHED IMPRP
> > ELECT VDW BOUNDARY MISC KINETIC
> > TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
> > PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2148000
> > ENERGY: 2149000 18052.3050 21410.8477 6868.9800 307.4126
> > -150538.9168 4629.4826 0.0000 0.0000 52071.9941
> > -47197.8948 300.6853 -46565.5396 -46551.0697 300.1125
> > 1143.6069 -47.5449 763614.3676 -232.5036 -233.2810
> >
> > ENERGY: 2150000 17945.8022 21549.3599 6870.9434 288.9983
> > -150534.9575 4506.9330 0.0000 0.0000 51973.1307
> > -47399.7900 300.1144 -46768.2908 -46745.8632 299.9337
> > 1371.6352 140.3605 763614.3676 -113.9294 -113.8836
> >
> > ENERGY: 2151000 17948.7143 21553.0049 6872.5997 300.8513
> > -150241.4487 4387.0052 0.0000 0.0000 51681.8177
> > -47497.4556 298.4322 -46855.6487 -46879.0623 299.4887
> > 1128.5691 -155.0570 763614.3676 -141.8838 -141.4656
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2151000
> > WRITING COORDINATES TO DCD FILE AT STEP 2152000
> > ENERGY: 2152000 17965.3541 21281.6639 6936.9223 307.3712
> > -149978.7718 4293.7936 0.0000 0.0000 51936.9174
> > -47256.7492 299.9053 -46614.8149 -46633.7004 299.8791
> > 1044.2784 -260.6070 763614.3676 -154.9321 -155.5537
> >
> > ENERGY: 2153000 18060.6980 21520.9055 6866.0695 300.7993
> > -150573.9400 4459.9516 0.0000 0.0000 52007.4160
> > -47358.1000 300.3124 -46725.1838 -46704.0960 299.4555
> > 719.8347 -233.1753 763614.3676 -176.5530 -175.8184
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2153000
> > ENERGY: 2154000 18035.7106 21718.2261 6895.7286 316.1919
> > -150470.3652 4564.1296 0.0000 0.0000 52079.3165
> > -46861.0620 300.7276 -46224.6220 -46211.0634 300.4939
> > 884.2597 -87.9826 763614.3676 -150.3208 -150.6103
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2154000
> > ENERGY: 2155000 18013.6477 21469.2460 6851.1778 320.4497
> > -150478.9898 4837.3102 0.0000 0.0000 51923.4630
> > -47063.6954 299.8276 -46421.5606 -46427.7576 300.7009
> > 1372.4797 -29.3345 763614.3676 -119.2887 -119.8083
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2155000
> > WRITING COORDINATES TO DCD FILE AT STEP 2156000
> > ENERGY: 2156000 18001.8450 21419.8714 6936.3037 297.7033
> > -149984.4667 4339.9950 0.0000 0.0000 51987.5020
> > -47001.2462 300.1974 -46363.8294 -46362.7071 300.2077
> > 1006.2176 -177.5357 763614.3676 -238.5271 -237.5715
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2157000
> > ENERGY: 2157000 17910.1799 21516.9479 6961.0451 293.4251
> > -149824.1432 4310.4109 0.0000 0.0000 52269.4700
> > -46562.6642 301.8256 -45924.2914 -45922.1478 301.1870
> > 1036.7141 -219.0950 763614.3676 -197.7857 -197.1263
> >
> > WRITING COORDINATES TO DCD FILE AT STEP 2158000
> > ENERGY: 2158000 17947.1297 21579.6281 6955.3950 277.4665
> > -150346.5553 4532.2800 0.0000 0.0000 52073.9913
> > -46980.6646 300.6968 -46350.8408 -46320.5343 300.9598
> > 923.7668 -240.3544 763614.3676 -189.0914 -189.2197
> >
> > ENERGY: 2159000 18192.4615 21402.9388 6931.4626 308.3835
> > -150535.5131 4534.7400 0.0000 0.0000 51857.9411
> > -47307.5855 299.4492 -46669.4940 -46660.0231 300.3176
> > 808.6854 -256.0078 763614.3676 -197.2923 -196.6459
> >
> > ENERGY: 2160000 18166.5506 21589.6236 6974.0475 301.2992
> > -150961.9812 4703.7496 0.0000 0.0000 51836.9603
> > -47389.7503 299.3281 -46751.5715 -46758.7688 299.5144
> > 823.7860 -151.0411 763614.3676 -183.7636 -184.1792
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:04 CST