From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Wed Sep 05 2007 - 11:02:21 CDT
Hi Peter,
I looked at the xst file and nothing seems to be changing for the
equilibration as you can see below:
16000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
17000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
18000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
19000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
20000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
21000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
22000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
23000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
24000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
25000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
26000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
27000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
28000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
29000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
30000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
31000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
32000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
33000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
34000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
35000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
36000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
37000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
38000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
39000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
40000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
41000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
42000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
43000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
44000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
45000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
46000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
47000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
48000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
49000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
50000 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437
And for the production run.. there are some changes.. but nothing major (or
so it seems to me)
# NAMD extended system trajectory file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z
s_u s_v s_w
0 70.3867 0 0 0 73.0221 0 0 0 75.7492 30.5597 30.3731 17.1437 0 0 0 0 0 0
1000 76.134 0 0 0 78.9845 0 0 0 81.9343 30.5597 30.3731 17.1437 3.26389e-05
3.26389e-05 3.26389e-05 0 0 0
2000 77.2681 0 0 0 80.1612 0 0 0 83.1549 30.5597 30.3731 17.1437 6.15032e-06
6.15032e-06 6.15032e-06 0 0 0
3000 78.2254 0 0 0 81.1543 0 0 0 84.1851 30.5597 30.3731 17.1437 1.90994e-05
1.90994e-05 1.90994e-05 0 0 0
4000 78.6539 0 0 0 81.5988 0 0 0 84.6462 30.5597 30.3731 17.1437 2.28707e-06
2.28707e-06 2.28707e-06 0 0 0
5000 79.1258 0 0 0 82.0884 0 0 0 85.1541 30.5597 30.3731 17.1437 -
9.26958e-06 -9.26958e-06 -9.26958e-06 0 0 0
6000 79.6063 0 0 0 82.5869 0 0 0 85.6712 30.5597 30.3731 17.1437 -
2.57472e-05 -2.57472e-05 -2.57472e-05 0 0 0
7000 79.2868 0 0 0 82.2554 0 0 0 85.3273 30.5597 30.3731 17.1437 1.23275e-05
1.23275e-05 1.23275e-05 0 0 0
8000 79.4456 0 0 0 82.4202 0 0 0 85.4983 30.5597 30.3731 17.1437 -1.2281e-05-
1.2281e-05 -1.2281e-05 0 0 0
9000 79.533 0 0 0 82.5109 0 0 0 85.5923 30.5597 30.3731 17.1437 -1.69753e-05-
1.69753e-05 -1.69753e-05 0 0 0
10000 79.7575 0 0 0 82.7438 0 0 0 85.834 30.5597 30.3731 17.1437 -
1.51208e-05 -1.51208e-05 -1.51208e-05 0 0 0
11000 79.8398 0 0 0 82.8292 0 0 0 85.9225 30.5597 30.3731 17.1437
2.22745e-05 2.22745e-05 2.22745e-05 0 0 0
12000 79.3917 0 0 0 82.3642 0 0 0 85.4402 30.5597 30.3731 17.1437 1.3142e-05
1.3142e-05 1.3142e-05 0 0 0
13000 79.7604 0 0 0 82.7467 0 0 0 85.837 30.5597 30.3731 17.1437 4.40619e-05
4.40619e-05 4.40619e-05 0 0 0
14000 79.6449 0 0 0 82.6269 0 0 0 85.7127 30.5597 30.3731 17.1437
3.90821e-05 3.90821e-05 3.90821e-05 0 0 0
15000 79.5816 0 0 0 82.5613 0 0 0 85.6446 30.5597 30.3731 17.1437 -
4.21917e-06 -4.21917e-06 -4.21917e-06 0 0 0
16000 79.579 0 0 0 82.5585 0 0 0 85.6418 30.5597 30.3731 17.1437 1.61066e-05
1.61066e-05 1.61066e-05 0 0 0
17000 79.4955 0 0 0 82.472 0 0 0 85.552 30.5597 30.3731 17.1437 -1.47335e-05-
1.47335e-05 -1.47335e-05 0 0 0
18000 79.4019 0 0 0 82.3748 0 0 0 85.4512 30.5597 30.3731 17.1437
1.33938e-06 1.33938e-06 1.33938e-06 0 0 0
19000 79.9046 0 0 0 82.8964 0 0 0 85.9923 30.5597 30.3731 17.1437
5.09923e-06 5.09923e-06 5.09923e-06 0 0 0
20000 79.4622 0 0 0 82.4374 0 0 0 85.5161 30.5597 30.3731 17.1437 -
1.38017e-05 -1.38017e-05 -1.38017e-05 0 0 0
21000 79.7705 0 0 0 82.7573 0 0 0 85.8479 30.5597 30.3731 17.1437 -
2.23141e-06 -2.23141e-06 -2.23141e-06 0 0 0
22000 79.7743 0 0 0 82.7611 0 0 0 85.852 30.5597 30.3731 17.1437 1.17119e-05
1.17119e-05 1.17119e-05 0 0 0
23000 79.6638 0 0 0 82.6466 0 0 0 85.7331 30.5597 30.3731 17.1437
3.21288e-05 3.21288e-05 3.21288e-05 0 0 0
24000 79.9108 0 0 0 82.9028 0 0 0 85.9989 30.5597 30.3731 17.1437
3.12021e-05 3.12021e-05 3.12021e-05 0 0 0
25000 79.8132 0 0 0 82.8015 0 0 0 85.8938 30.5597 30.3731 17.1437 -
2.40582e-05 -2.40582e-05 -2.40582e-05 0 0 0
26000 79.9671 0 0 0 82.9612 0 0 0 86.0595 30.5597 30.3731 17.1437
1.15954e-05 1.15954e-05 1.15954e-05 0 0 0
27000 79.8979 0 0 0 82.8894 0 0 0 85.985 30.5597 30.3731 17.1437 2.14748e-05
2.14748e-05 2.14748e-05 0 0 0
645000 80.189 0 0 0 83.1914 0 0 0 86.2983 30.5597 30.3731 17.1437
1.31228e-05 1.31228e-05 1.31228e-05 0 0 0
646000 79.9343 0 0 0 82.9272 0 0 0 86.0242 30.5597 30.3731 17.1437
2.83692e-05 2.83692e-05 2.83692e-05 0 0 0
647000 80.0714 0 0 0 83.0694 0 0 0 86.1717 30.5597 30.3731 17.1437 -
3.90748e-06 -3.90748e-06 -3.90748e-06 0 0 0
648000 79.7779 0 0 0 82.7649 0 0 0 85.8559 30.5597 30.3731 17.1437 -
1.33286e-05 -1.33286e-05 -1.33286e-05 0 0 0
649000 79.8803 0 0 0 82.8711 0 0 0 85.9661 30.5597 30.3731 17.1437 -
1.48133e-05 -1.48133e-05 -1.48133e-05 0 0 0
650000 80.0967 0 0 0 83.0956 0 0 0 86.1989 30.5597 30.3731 17.1437 -
2.71452e-05 -2.71452e-05 -2.71452e-05 0 0 0
651000 79.7049 0 0 0 82.6892 0 0 0 85.7774 30.5597 30.3731 17.1437 -
5.44663e-05 -5.44663e-05 -5.44663e-05 0 0 0
652000 79.952 0 0 0 82.9456 0 0 0 86.0433 30.5597 30.3731 17.1437
3.41408e-06 3.41408e-06 3.41408e-06 0 0 0
653000 79.8053 0 0 0 82.7933 0 0 0 85.8854 30.5597 30.3731 17.1437 -
4.96035e-05 -4.96035e-05 -4.96035e-05 0 0 0
654000 80.3898 0 0 0 83.3997 0 0 0 86.5144 30.5597 30.3731 17.1437
2.12467e-06 2.12467e-06 2.12467e-06 0 0 0
655000 80.1867 0 0 0 83.189 0 0 0 86.2958 30.5597 30.3731 17.1437
1.85785e-05 1.85785e-05 1.85785e-05 0 0 0
656000 80.1883 0 0 0 83.1906 0 0 0 86.2975 30.5597 30.3731 17.1437
1.51099e-05 1.51099e-05 1.51099e-05 0 0 0
657000 79.9199 0 0 0 82.9122 0 0 0 86.0087 30.5597 30.3731 17.1437 -
4.64262e-06 -4.64262e-06 -4.64262e-06 0 0 0
658000 80.2277 0 0 0 83.2316 0 0 0 86.34 30.5597 30.3731 17.1437 5.71878e-05
5.71878e-05 5.71878e-05 0 0 0
659000 79.843 0 0 0 82.8324 0 0 0 85.9259 30.5597 30.3731 17.1437
1.79714e-05 1.79714e-05 1.79714e-05 0 0 0
660000 79.8746 0 0 0 82.8653 0 0 0 85.96 30.5597 30.3731 17.1437 -
2.37135e-06 -2.37135e-06 -2.37135e-06 0 0 0
661000 79.962 0 0 0 82.9559 0 0 0 86.054 30.5597 30.3731 17.1437 5.17482e-06
5.17482e-06 5.17482e-06 0 0 0
662000 79.8803 0 0 0 82.8712 0 0 0 85.9661 30.5597 30.3731 17.1437 -
6.81252e-07 -6.81252e-07 -6.81252e-07 0 0 0
663000 79.857 0 0 0 82.847 0 0 0 85.9411 30.5597 30.3731 17.1437 3.63852e-05
3.63852e-05 3.63852e-05 0 0 0
664000 79.9647 0 0 0 82.9588 0 0 0 86.0569 30.5597 30.3731 17.1437
1.06011e-05 1.06011e-05 1.06011e-05 0 0 0
665000 79.7353 0 0 0 82.7207 0 0 0 85.81 30.5597 30.3731 17.1437 -
6.62087e-05 -6.62087e-05 -6.62087e-05 0 0 0
666000 79.671 0 0 0 82.654 0 0 0 85.7408 30.5597 30.3731 17.1437 -
2.98215e-05 -2.98215e-05 -2.98215e-05 0 0 0
667000 79.3863 0 0 0 82.3586 0 0 0 85.4344 30.5597 30.3731 17.1437
1.94912e-05 1.94912e-05 1.94912e-05 0 0 0
670,1 Bot
Thanks,
Arun
On 9/6/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Hi Arun,
> you might just want to start by looking at the box volume (from the xst
> file), and how it varies with temperature. To get the water density, you
> need to take those box volumes and subtract the protein volume (I
> believe you can get this using MSMS, or from the server at
> http://molbio.info.nih.gov/structbio/basic.html). This should let you
> calculate the water density fairly easily. Large volume fluctuations in
> an NPT md simulation can do odd things to the dynamics, which is why I'm
> curious whether the volume varied as much in your case as it did in the
> paper you cited.
> Peter
>
>
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