[gmx-users] Vacuum disappear after NPT equilibration?
Justin Lemkul
jalemkul at vt.edu
Fri Jan 17 19:49:04 CET 2014
On 1/17/14, 1:43 PM, Guangwei Jiang wrote:
> Dear all,
>
> I have built a system with the lipid bilayers and water molecules in the centre. Besides, two vacuum spaces above and under this target are introduced to separate the molecules flowing from the two sides.
>
> But when I start the NPT equilibration, the vacuum space gets smaller and smaller and finally disappeared. The box factors are pasted below to show the changing. Since I am new to GROMACS, can anyone tell me the reason to that and how to maintain the vacuum space?
>
In a battle between 1 atm of pressure vs. nothing, 1 atm of pressure always wins :)
If you need to maintain void space, you need to either make the box
incompressible along the desired axis (assuming that is z in this case) or use
NVT so the box does not change over time.
-Justin
> Thanks very much!
>
> Best wishes,
> Guangwei Jiang
>
>
> ---------------------------------------------------------------------------------------------------------------------
>
> 0 6.4184 6.4435 12.5966 0 0 0
> 0.2 6.41822 6.44332 12.5964 0 0 0
> 0.4 6.41706 6.44216 12.5958 0 0 0
> 0.6 6.41522 6.4403 12.5947 0 0 0
> 0.8 6.4129 6.43797 12.5932 0 0 0
> 1 6.41017 6.43523 12.5913 0 0 0
> 1.2 6.40754 6.4326 12.5897 0 0 0
> 1.4 6.4049 6.42994 12.588 0 0 0
> 1.6 6.40219 6.42723 12.586 0 0 0
> 1.8 6.39975 6.42478 12.5838 0 0 0
> 2 6.39724 6.42226 12.581 0 0 0
> 2.2 6.39453 6.41953 12.5779 0 0 0
> 2.4 6.39217 6.41716 12.5745 0 0 0
> 2.6 6.3902 6.41519 12.5708 0 0 0
> 2.8 6.38803 6.41301 12.5667 0 0 0
> 3 6.38594 6.41091 12.5624 0 0 0
> 3.2 6.38436 6.40933 12.5577 0 0 0
> 3.4 6.38282 6.40778 12.5528 0 0 0
> 3.6 6.38127 6.40622 12.5477 0 0 0
> 3.8 6.37971 6.40466 12.5421 0 0 0
> 4 6.37802 6.40296 12.5362 0 0 0
> 4.2 6.37659 6.40153 12.5303 0 0 0
> 4.4 6.37525 6.40018 12.5242 0 0 0
> 4.6 6.37417 6.39909 12.518 0 0 0
> 4.8 6.37328 6.3982 12.5117 0 0 0
> 5 6.37269 6.39762 12.5051 0 0 0
> 5.2 6.37259 6.39751 12.4984 0 0 0
> 5.4 6.37265 6.39757 12.4917 0 0 0
> 5.6 6.37277 6.39769 12.4847 0 0 0
> 5.8 6.37293 6.39785 12.4774 0 0 0
> 6 6.37295 6.39787 12.4699 0 0 0
> 6.2 6.37282 6.39774 12.4626 0 0 0
> 6.4 6.3721 6.39702 12.4547 0 0 0
> 6.6 6.37142 6.39633 12.4466 0 0 0
> 6.8 6.37081 6.39573 12.4381 0 0 0
> 7 6.37034 6.39525 12.4296 0 0 0
> 7.2 6.36943 6.39434 12.4208 0 0 0
> 7.4 6.36834 6.39324 12.4118 0 0 0
> 7.6 6.36681 6.39171 12.4019 0 0 0
> 7.8 6.36477 6.38966 12.3913 0 0 0
> 8 6.3625 6.38738 12.3804 0 0 0
> 8.2 6.3598 6.38468 12.3687 0 0 0
> 8.4 6.35656 6.38142 12.3561 0 0 0
> 8.6 6.35292 6.37777 12.3426 0 0 0
> 8.8 6.34929 6.37412 12.3287 0 0 0
> 9 6.34612 6.37093 12.3149 0 0 0
> 9.2 6.34322 6.36802 12.3008 0 0 0
> 9.4 6.34071 6.3655 12.2863 0 0 0
> 9.6 6.33849 6.36328 12.2715 0 0 0
> 9.8 6.33597 6.36075 12.2561 0 0 0
> 10 6.33334 6.35811 12.24 0 0 0
> 10.2 6.33147 6.35623 12.2236 0 0 0
> 10.4 6.33033 6.35508 12.2071 0 0 0
> 10.6 6.32998 6.35474 12.1908 0 0 0
> 10.8 6.32983 6.35458 12.1741 0 0 0
> 11 6.33003 6.35478 12.1575 0 0 0
> 11.2 6.33037 6.35512 12.1406 0 0 0
> 11.4 6.3304 6.35515 12.1234 0 0 0
> 11.6 6.33048 6.35523 12.1062 0 0 0
> 11.8 6.33067 6.35543 12.0889 0 0 0
> 12 6.33137 6.35613 12.0717 0 0 0
> 12.2 6.33227 6.35703 12.0542 0 0 0
> 12.4 6.33353 6.3583 12.0363 0 0 0
> 12.6 6.33458 6.35935 12.0181 0 0 0
> 12.8 6.33508 6.35985 11.9993 0 0 0
> 13 6.33507 6.35985 11.98 0 0 0
> 13.2 6.33498 6.35976 11.9604 0 0 0
> 13.4 6.33478 6.35956 11.9405 0 0 0
> 13.6 6.33366 6.35843 11.9202 0 0 0
> 13.8 6.33165 6.35642 11.8993 0 0 0
> 14 6.32908 6.35383 11.8779 0 0 0
> 14.2 6.32638 6.35112 11.8563 0 0 0
> 14.4 6.32316 6.34789 11.8341 0 0 0
> 14.6 6.3198 6.34452 11.8111 0 0 0
> 14.8 6.31646 6.34117 11.7876 0 0 0
> 15 6.31316 6.33785 11.7633 0 0 0
> 15.2 6.30998 6.33466 11.7387 0 0 0
> 15.4 6.3072 6.33187 11.7138 0 0 0
> 15.6 6.30473 6.32939 11.6885 0 0 0
> 15.8 6.30252 6.32716 11.6628 0 0 0
> 16 6.30031 6.32495 11.6368 0 0 0
> 16.2 6.29847 6.3231 11.6106 0 0 0
> 16.4 6.29721 6.32184 11.5842 0 0 0
> 16.6 6.29634 6.32096 11.5579 0 0 0
> 16.8 6.29605 6.32068 11.5314 0 0 0
> 17 6.29608 6.3207 11.5043 0 0 0
> 17.2 6.29612 6.32075 11.477 0 0 0
> 17.4 6.29627 6.3209 11.4491 0 0 0
> 17.6 6.29666 6.32129 11.4208 0 0 0
> 17.8 6.29744 6.32207 11.3924 0 0 0
> 18 6.29833 6.32296 11.3631 0 0 0
> 18.2 6.29912 6.32375 11.3328 0 0 0
> 18.4 6.29984 6.32448 11.302 0 0 0
> 18.6 6.30035 6.32498 11.2707 0 0 0
> 18.8 6.30094 6.32558 11.2394 0 0 0
> 19 6.30114 6.32578 11.208 0 0 0
> 19.2 6.3012 6.32584 11.1764 0 0 0
> 19.4 6.30137 6.32601 11.145 0 0 0
> 19.6 6.30115 6.3258 11.1131 0 0 0
> 19.8 6.30033 6.32497 11.0807 0 0 0
> 20 6.29891 6.32354 11.0474 0 0 0
> 20.2 6.29729 6.32192 11.0136 0 0 0
> 20.4 6.29577 6.32039 10.9794 0 0 0
> 20.6 6.29438 6.319 10.9451 0 0 0
> 20.8 6.29266 6.31727 10.9104 0 0 0
> 21 6.2908 6.3154 10.8754 0 0 0
> 21.2 6.28841 6.313 10.8395 0 0 0
> 21.4 6.28589 6.31047 10.8028 0 0 0
> 21.6 6.28307 6.30764 10.7654 0 0 0
> 21.8 6.28029 6.30485 10.7272 0 0 0
> 22 6.27805 6.3026 10.689 0 0 0
> 22.2 6.27554 6.30008 10.6503 0 0 0
> 22.4 6.27282 6.29735 10.6109 0 0 0
> 22.6 6.27031 6.29483 10.5713 0 0 0
> 22.8 6.26812 6.29264 10.5312 0 0 0
> 23 6.26569 6.29019 10.4911 0 0 0
> 23.2 6.26347 6.28796 10.4508 0 0 0
> 23.4 6.26137 6.28585 10.4098 0 0 0
> 23.6 6.25958 6.28406 10.3685 0 0 0
> 23.8 6.25854 6.28302 10.3275 0 0 0
> 24 6.25779 6.28226 10.2864 0 0 0
> 24.2 6.25734 6.28181 10.2449 0 0 0
> 24.4 6.25672 6.28119 10.2026 0 0 0
> 24.6 6.25577 6.28024 10.1598 0 0 0
> 24.8 6.25407 6.27853 10.1164 0 0 0
> 25 6.2518 6.27624 10.0724 0 0 0
> 25.2 6.24873 6.27316 10.0276 0 0 0
> 25.4 6.24494 6.26937 9.98188 0 0 0
> 25.6 6.24052 6.26492 9.93569 0 0 0
> 25.8 6.23596 6.26035 9.88899 0 0 0
> 26 6.23215 6.25653 9.84199 0 0 0
> 26.2 6.228 6.25236 9.79412 0 0 0
> 26.4 6.22384 6.24818 9.74592 0 0 0
> 26.6 6.21983 6.24416 9.69669 0 0 0
> 26.8 6.2159 6.2402 9.64641 0 0 0
> 27 6.21251 6.2368 9.59591 0 0 0
> 27.2 6.21031 6.23459 9.54524 0 0 0
> 27.4 6.20838 6.23266 9.49369 0 0 0
> 27.6 6.20647 6.23074 9.44129 0 0 0
> 27.8 6.20339 6.22765 9.38719 0 0 0
> 28 6.2001 6.22434 9.33221 0 0 0
> 28.2 6.19698 6.22121 9.27618 0 0 0
> 28.4 6.19443 6.21866 9.21995 0 0 0
> 28.6 6.19251 6.21673 9.16308 0 0 0
> 28.8 6.19083 6.21504 9.10538 0 0 0
> 29 6.18955 6.21375 9.04693 0 0 0
> 29.2 6.18843 6.21263 8.98765 0 0 0
> 29.4 6.1877 6.2119 8.92744 0 0 0
> 29.6 6.18717 6.21137 8.86707 0 0 0
> 29.8 6.18564 6.20983 8.80524 0 0 0
> 30 6.18351 6.20769 8.74186 0 0 0
> 30.2 6.18093 6.2051 8.67763 0 0 0
> 30.4 6.17824 6.2024 8.61307 0 0 0
> 30.6 6.17601 6.20016 8.54854 0 0 0
> 30.8 6.17444 6.19858 8.48448 0 0 0
> 31 6.17294 6.19708 8.42004 0 0 0
> 31.2 6.17164 6.19578 8.35426 0 0 0
> 31.4 6.17023 6.19436 8.28761 0 0 0
> 31.6 6.16864 6.19276 8.21973 0 0 0
> 31.8 6.167 6.19112 8.15094 0 0 0
> 32 6.16565 6.18976 8.08189 0 0 0
> 32.2 6.16394 6.18805 8.01255 0 0 0
> 32.4 6.16211 6.18621 7.94196 0 0 0
> 32.6 6.15945 6.18354 7.86984 0 0 0
> 32.8 6.15652 6.18059 7.79584 0 0 0
> 33 6.15352 6.17758 7.72051 0 0 0
> 33.2 6.15018 6.17423 7.64373 0 0 0
> 33.4 6.14602 6.17006 7.56558 0 0 0
> 33.6 6.14138 6.16539 7.4863 0 0 0
> 33.8 6.13655 6.16054 7.40553 0 0 0
> 34 6.13242 6.1564 7.32539 0 0 0
> 34.2 6.12871 6.15268 7.24498 0 0 0
> 34.4 6.12589 6.14984 7.16398 0 0 0
> 34.6 6.12426 6.14821 7.08207 0 0 0
>
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
==================================================
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