RE: high (or low) pressure readings

From: carlos n. a. (carlosjavierna_at_hotmail.com)
Date: Mon Dec 13 2004 - 13:36:10 CST

Hi. maybe you can read this

http://amber.scripps.edu/Questions/mail/32.html
http://amber.scripps.edu/Questions/pressure.html

>From: Charles Danko <dankoc_at_gmail.com>
>Reply-To: Charles Danko <dankoc_at_gmail.com>
>To: namd-l_at_ks.uiuc.edu
>Subject: namd-l: high (or low) pressure readings
>Date: Mon, 13 Dec 2004 10:42:52 -0500
>
>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

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