From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Sep 05 2007 - 11:32:58 CDT
Hi Arun,
rather silly of me; you can also read the volume directly from the log
file. Nevertheless, there's a 1.4x increase in system volume that
occurs during your production run, which is fairly significant. Out of
curiosity, is there any reason you didn't also equilibrate at 520K in
NPT? The config file you posted has the piston turned off, although your
simulation summary listed this as NPT. It's probably not ideal to have
such a large volume adjustment occur during a production run.
I don't see any serious problems in your simulation that would lead to
wrong results though. Unfortunately, there isn't quite enough
information in the methods section of that unfolding paper you're
comparing your results with to ensure that you're using identical
conditions; certainly the system size is different, and they don't
mention the thermostat or barostat being used, for example. Do you see
any kind of progressive unfolding in your simulations, even if it is
slower than the 1 ns they reported?
Best,
Peter
Arun Krishnan wrote:
> 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
> <mailto: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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