From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Dec 14 2004 - 11:45:13 CST
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 - 15:39:03 CST