From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon Dec 13 2004 - 11:13:42 CST
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
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 **
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