From: Xiaoqing Wang (namdwxq_at_126.com)
Date: Tue Jul 26 2005 - 22:02:34 CDT
Dear,
Thank you very much for your explanation.
The PRESSAVG and GPRESSAVG values are close to 1 atm in the end. But I
don't know why the system becomes dispersing completely. The input file
"equil.namd" and xst file "equil_out.xst" are enclosed. Does it arise
from the pressure or some others?
When I calculate the same input files by using "namd2" which I
downloaded binary of "Linux-i686" from web site :
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD
the unitcell of the system is close to the original value.
Any tips would be greatly appreciated!
Sincerely,
Xiaoqing
在2005年07月27日的01:20，nordgren_at_sas.upenn.edu写道：
> The NAMD units of pressure are indeed in bars.
>
> However, in a typical constant-pressure simulation, the short-term average
> pressure of the system (PRESSAVG) will typically fluctuate by hundreds of
> bars, and the instantaneous value (PRESSURE) will often be in the thousands.
>
> Moreover, you *may* see PRESSURE values that can look quite large (say, in
> the tens of thousands) -- if you are using multiple-timestepping, but
> printing energies every step. This is because the long-range forces are not
> being computed every step, and so when you look at the instantaneous pressure
> during those off-steps, the numbers look pretty wild. (But it all comes out
> correctly in the end.)
>
> IMO, the only parameter really worth paying much attention to is "PRESSAVG"
> (or better, "GPRESSAVG"), and even then it is most meaningful when you look
> at its longer-term average trend (which *should* be close to your specified
> value of 1 atm or whatever).
>
> hope this helps...
>
> C. Erik Nordgren, Ph.D.
> Department of Chemistry
> University of Pennsylvania
>
>
> Quoting Xiaoqing Wang <namdwxq_at_126.com>:
>
> > Hi,
> >
> > What's the unit of the item PRESSURE of output file?
> > In the equil.namd input script file the LangevinPistonTarget is set to
> > 1.01325(bar). In my output file the PRESSURE is about 0 in the end. But
> > in the output(equil.log) file which I downloaded from
> > http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/sample/
> > the PRESSURE value is about 1000 in the end.
> >
> > Sincerely,
> > Xiaoqing
> >
> >
> > å¨2005å¹´07æ25æ¥ç11:06ï¼Xiaoqing Wangåéï¼
> > > Dear all,
> > >
> > > I downloaded "fftw-linux-amd64.tar.gz" and "tcl-linux-amd64.tar.gz" from
> > > http://www.ks.uiuc.edu/Research/namd/libraries/ and plugins for
> > > LINUXAMD64 and "charm-net-linux-amd64.tar.gz" from
> > > http://charm.cs.uiuc.edu/autobuild/bin/ and NAMD_2.5_Source.tar.gz.
> > >
> > > I compiled NAMD with
> > > ./config tcl fftw plugins Linux-amd64-g++
> > > ./make
> > >
> > > I download input files from web site :
> > > http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/sample/
> > > and run "namd2 equil.namd>equil.log" on AMD64 opteron.
> > >
> > > When run equilibrate with langevinPiston on
> > > ---------------------------------------------
> > > # equilibrate volume with CAs restrained
> > > langevinPiston on
> > > run 5000
> > > output equil_ca
> > > ---------------------------------------------
> > > the systerm becomes very large and disperse.
> > >
> > > I compiled many times and run many other examples and found that all of
> > > the systerms become disperse when set "langevinpiston on". I don't know
> > > why the pressure value is incorrect and the pressure control can't work.
> > >
> > >
> > > Any tips would be greatly appreciated!
> > >
> > --Xiaoqing
> > Wuhan University
> > Wuhan 430072
> > China
>
-- --Xiaoqing Wuhan University Wuhan 430072 China
# 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
2000 30 0 0 15 25.98 0 0 0 64 0 0 0
2100 30 0 0 15 25.98 0 0 0 64 0 0 0
2200 30 0 0 15 25.98 0 0 0 64 0 0 0
2300 30 0 0 15 25.98 0 0 0 64 0 0 0
2400 30 0 0 15 25.98 0 0 0 64 0 0 0
2500 30 0 0 15 25.98 0 0 0 64 0 0 0
2600 30 0 0 15 25.98 0 0 0 64 0 0 0
2700 30 0 0 15 25.98 0 0 0 64 0 0 0
2800 30 0 0 15 25.98 0 0 0 64 0 0 0
2900 30 0 0 15 25.98 0 0 0 64 0 0 0
3000 30 0 0 15 25.98 0 0 0 64 0 0 0
3100 30 0 0 15 25.98 0 0 0 64 0 0 0
3200 30 0 0 15 25.98 0 0 0 64 0 0 0
3300 30 0 0 15 25.98 0 0 0 64 0 0 0
3400 30 0 0 15 25.98 0 0 0 64 0 0 0
3500 30 0 0 15 25.98 0 0 0 64 0 0 0
3600 30 0 0 15 25.98 0 0 0 64 0 0 0
3700 30 0 0 15 25.98 0 0 0 64 0 0 0
3800 30 0 0 15 25.98 0 0 0 64 0 0 0
3900 30 0 0 15 25.98 0 0 0 64 0 0 0
4000 30 0 0 15 25.98 0 0 0 64 0 0 0
4100 30 0 0 15 25.98 0 0 0 64 0 0 0
4200 30 0 0 15 25.98 0 0 0 64 0 0 0
4300 30 0 0 15 25.98 0 0 0 64 0 0 0
4400 30 0 0 15 25.98 0 0 0 64 0 0 0
4500 30 0 0 15 25.98 0 0 0 64 0 0 0
4600 30 0 0 15 25.98 0 0 0 64 0 0 0
4700 30 0 0 15 25.98 0 0 0 64 0 0 0
4800 30 0 0 15 25.98 0 0 0 64 0 0 0
4900 30 0 0 15 25.98 0 0 0 64 0 0 0
5000 30 0 0 15 25.98 0 0 0 64 0 0 0
5000 30 0 0 15 25.98 0 0 0 64 0 0 0 0 0 0 0 0 0
5100 30.7168 0 0 15.3584 26.6008 0 0 0 65.5292 0 0 0 0.000288232 0.000288232 0.000288232 0 0 0
5200 31.193 0 0 15.5965 27.0131 0 0 0 66.5451 0 0 0 0.000278537 0.000278537 0.000278537 0 0 0
5300 31.6145 0 0 15.8073 27.3782 0 0 0 67.4443 0 0 0 0.000163072 0.000163072 0.000163072 0 0 0
5400 31.8896 0 0 15.9448 27.6164 0 0 0 68.0312 0 0 0 0.000100397 0.000100397 0.000100397 0 0 0
5500 32.2902 0 0 16.1451 27.9633 0 0 0 68.8858 0 0 0 1.34967e-05 1.34967e-05 1.34967e-05 0 0 0
5600 32.603 0 0 16.3015 28.2342 0 0 0 69.5531 0 0 0 2.31163e-05 2.31163e-05 2.31163e-05 0 0 0
5700 32.856 0 0 16.428 28.4533 0 0 0 70.0927 0 0 0 0.000112712 0.000112712 0.000112712 0 0 0
5800 33.1994 0 0 16.5997 28.7507 0 0 0 70.8254 0 0 0 5.67145e-05 5.67145e-05 5.67145e-05 0 0 0
5900 33.6019 0 0 16.801 29.0993 0 0 0 71.6841 0 0 0 0.000124127 0.000124127 0.000124127 0 0 0
6000 34.0343 0 0 17.0172 29.4737 0 0 0 72.6065 0 0 0 0.000174754 0.000174754 0.000174754 0 0 0
6100 34.4444 0 0 17.2222 29.8289 0 0 0 73.4815 0 0 0 0.000227149 0.000227149 0.000227149 0 0 0
6200 34.665 0 0 17.3325 30.0199 0 0 0 73.952 0 0 0 0.000120525 0.000120525 0.000120525 0 0 0
6300 35.1862 0 0 17.5931 30.4712 0 0 0 75.0639 0 0 0 8.47655e-05 8.47655e-05 8.47655e-05 0 0 0
6400 35.6303 0 0 17.8152 30.8559 0 0 0 76.0113 0 0 0 0.000118728 0.000118728 0.000118728 0 0 0
6500 36.0882 0 0 18.0441 31.2524 0 0 0 76.9883 0 0 0 -1.18927e-06 -1.18927e-06 -1.18927e-06 0 0 0
6600 36.6558 0 0 18.3279 31.7439 0 0 0 78.1991 0 0 0 3.20344e-05 3.20344e-05 3.20344e-05 0 0 0
6700 37.2923 0 0 18.6461 32.2951 0 0 0 79.5568 0 0 0 0.000207344 0.000207344 0.000207344 0 0 0
6800 37.8943 0 0 18.9472 32.8165 0 0 0 80.8412 0 0 0 0.000169522 0.000169522 0.000169522 0 0 0
6900 38.4463 0 0 19.2231 33.2945 0 0 0 82.0187 0 0 0 0.000102878 0.000102878 0.000102878 0 0 0
7000 38.985 0 0 19.4925 33.761 0 0 0 83.168 0 0 0 0.00014018 0.00014018 0.00014018 0 0 0
7100 39.4859 0 0 19.743 34.1948 0 0 0 84.2367 0 0 0 0.000201866 0.000201866 0.000201866 0 0 0
7200 40.2622 0 0 20.1311 34.867 0 0 0 85.8926 0 0 0 0.000204328 0.000204328 0.000204328 0 0 0
7300 40.817 0 0 20.4085 35.3476 0 0 0 87.0763 0 0 0 0.000148415 0.000148415 0.000148415 0 0 0
7400 41.5172 0 0 20.7586 35.9539 0 0 0 88.57 0 0 0 0.000109782 0.000109782 0.000109782 0 0 0
7500 42.2747 0 0 21.1374 36.6099 0 0 0 90.1861 0 0 0 0.00026816 0.00026816 0.00026816 0 0 0
7600 43.0559 0 0 21.5279 37.2864 0 0 0 91.8525 0 0 0 0.000218858 0.000218858 0.000218858 0 0 0
7700 43.8628 0 0 21.9314 37.9852 0 0 0 93.5739 0 0 0 0.000148194 0.000148194 0.000148194 0 0 0
7800 44.6744 0 0 22.3372 38.6881 0 0 0 95.3055 0 0 0 0.000184362 0.000184362 0.000184362 0 0 0
7900 45.5447 0 0 22.7723 39.4417 0 0 0 97.162 0 0 0 0.000220461 0.000220461 0.000220461 0 0 0
8000 46.3604 0 0 23.1802 40.1481 0 0 0 98.9022 0 0 0 0.000189835 0.000189835 0.000189835 0 0 0
8100 47.2517 0 0 23.6259 40.92 0 0 0 100.804 0 0 0 4.6459e-05 4.6459e-05 4.6459e-05 0 0 0
8200 47.9803 0 0 23.9902 41.551 0 0 0 102.358 0 0 0 0.000314854 0.000314854 0.000314854 0 0 0
8300 49.026 0 0 24.513 42.4566 0 0 0 104.589 0 0 0 0.000181292 0.000181292 0.000181292 0 0 0
8400 50.0661 0 0 25.033 43.3572 0 0 0 106.808 0 0 0 0.000183141 0.000183141 0.000183141 0 0 0
8500 51.0163 0 0 25.5082 44.1802 0 0 0 108.835 0 0 0 0.00015682 0.00015682 0.00015682 0 0 0
8600 51.9618 0 0 25.9809 44.9989 0 0 0 110.852 0 0 0 0.000246461 0.000246461 0.000246461 0 0 0
8700 52.9975 0 0 26.4988 45.8958 0 0 0 113.061 0 0 0 0.000248652 0.000248652 0.000248652 0 0 0
8800 53.9389 0 0 26.9695 46.7111 0 0 0 115.07 0 0 0 0.000150681 0.000150681 0.000150681 0 0 0
8900 55.1429 0 0 27.5715 47.7538 0 0 0 117.638 0 0 0 0.00017959 0.00017959 0.00017959 0 0 0
9000 56.2235 0 0 28.1118 48.6896 0 0 0 119.943 0 0 0 0.000142895 0.000142895 0.000142895 0 0 0
9100 57.3735 0 0 28.6868 49.6855 0 0 0 122.397 0 0 0 0.000265366 0.000265366 0.000265366 0 0 0
9200 58.4955 0 0 29.2477 50.6571 0 0 0 124.79 0 0 0 0.000317673 0.000317673 0.000317673 0 0 0
9300 59.5446 0 0 29.7723 51.5656 0 0 0 127.028 0 0 0 0.000160057 0.000160057 0.000160057 0 0 0
9400 60.8069 0 0 30.4034 52.6587 0 0 0 129.721 0 0 0 0.000235716 0.000235716 0.000235716 0 0 0
9500 62.0416 0 0 31.0208 53.728 0 0 0 132.355 0 0 0 0.000128236 0.000128236 0.000128236 0 0 0
9600 63.2797 0 0 31.6399 54.8002 0 0 0 134.997 0 0 0 0.000243551 0.000243551 0.000243551 0 0 0
9700 64.6348 0 0 32.3174 55.9737 0 0 0 137.888 0 0 0 0.000180142 0.000180142 0.000180142 0 0 0
9800 65.7728 0 0 32.8864 56.9593 0 0 0 140.315 0 0 0 0.000146162 0.000146162 0.000146162 0 0 0
9900 67.169 0 0 33.5845 58.1683 0 0 0 143.294 0 0 0 0.000267576 0.000267576 0.000267576 0 0 0
10000 68.5971 0 0 34.2985 59.4051 0 0 0 146.34 0 0 0 0.000291267 0.000291267 0.000291267 0 0 0
10000 68.5971 0 0 34.2985 59.4051 0 0 0 146.34 0 0 0 0.000291267 0.000291267 0.000291267 0 0 0
10100 70.1236 0 0 35.0618 60.727 0 0 0 149.597 0 0 0 0.000166651 0.000166651 0.000166651 0 0 0
10200 71.8626 0 0 35.9313 62.233 0 0 0 153.307 0 0 0 0.000244688 0.000244688 0.000244688 0 0 0
10300 73.5488 0 0 36.7744 63.6932 0 0 0 156.904 0 0 0 0.000204267 0.000204267 0.000204267 0 0 0
10400 75.5435 0 0 37.7718 65.4207 0 0 0 161.159 0 0 0 0.000167839 0.000167839 0.000167839 0 0 0
10500 77.4141 0 0 38.7071 67.0406 0 0 0 165.15 0 0 0 0.00023829 0.00023829 0.00023829 0 0 0
10600 79.0962 0 0 39.5481 68.4973 0 0 0 168.739 0 0 0 0.000183797 0.000183797 0.000183797 0 0 0
10700 80.9974 0 0 40.4987 70.1437 0 0 0 172.794 0 0 0 0.000188956 0.000188956 0.000188956 0 0 0
10800 83.2053 0 0 41.6027 72.0558 0 0 0 177.505 0 0 0 0.000248128 0.000248128 0.000248128 0 0 0
10900 85.3355 0 0 42.6678 73.9006 0 0 0 182.049 0 0 0 0.000227292 0.000227292 0.000227292 0 0 0
11000 87.4728 0 0 43.7364 75.7514 0 0 0 186.609 0 0 0 0.000388683 0.000388683 0.000388683 0 0 0
11100 89.9912 0 0 44.9956 77.9324 0 0 0 191.981 0 0 0 0.000218473 0.000218473 0.000218473 0 0 0
11200 92.4629 0 0 46.2315 80.0729 0 0 0 197.254 0 0 0 0.000272762 0.000272762 0.000272762 0 0 0
11300 94.8735 0 0 47.4368 82.1605 0 0 0 202.397 0 0 0 0.000304065 0.000304065 0.000304065 0 0 0
11400 97.3378 0 0 48.6689 84.2945 0 0 0 207.654 0 0 0 0.000126896 0.000126896 0.000126896 0 0 0
11500 100.191 0 0 50.0954 86.7653 0 0 0 213.741 0 0 0 0.000295714 0.000295714 0.000295714 0 0 0
11600 102.738 0 0 51.3691 88.9713 0 0 0 219.175 0 0 0 0.000226749 0.000226749 0.000226749 0 0 0
11700 105.766 0 0 52.8831 91.5936 0 0 0 225.635 0 0 0 0.000239717 0.000239717 0.000239717 0 0 0
11800 108.309 0 0 54.1545 93.7956 0 0 0 231.059 0 0 0 0.000325317 0.000325317 0.000325317 0 0 0
11900 111.059 0 0 55.5296 96.1772 0 0 0 236.926 0 0 0 0.000179598 0.000179598 0.000179598 0 0 0
12000 114.293 0 0 57.1467 98.9781 0 0 0 243.826 0 0 0 0.000305071 0.000305071 0.000305071 0 0 0
12100 117.634 0 0 58.8172 101.871 0 0 0 250.953 0 0 0 0.000276023 0.000276023 0.000276023 0 0 0
12200 120.509 0 0 60.2543 104.36 0 0 0 257.085 0 0 0 0.000226923 0.000226923 0.000226923 0 0 0
12300 124.112 0 0 62.0558 107.481 0 0 0 264.771 0 0 0 0.000220361 0.000220361 0.000220361 0 0 0
12400 127.664 0 0 63.8322 110.557 0 0 0 272.351 0 0 0 0.000256628 0.000256628 0.000256628 0 0 0
12500 132.036 0 0 66.0182 114.344 0 0 0 281.678 0 0 0 0.000396001 0.000396001 0.000396001 0 0 0
12600 136.201 0 0 68.1007 117.95 0 0 0 290.563 0 0 0 0.000158258 0.000158258 0.000158258 0 0 0
12700 140.005 0 0 70.0023 121.244 0 0 0 298.677 0 0 0 0.000212215 0.000212215 0.000212215 0 0 0
12800 143.838 0 0 71.919 124.564 0 0 0 306.855 0 0 0 0.000243486 0.000243486 0.000243486 0 0 0
12900 148.218 0 0 74.1092 128.357 0 0 0 316.199 0 0 0 0.000281059 0.000281059 0.000281059 0 0 0
13000 152.548 0 0 76.274 132.107 0 0 0 325.436 0 0 0 0.000302771 0.000302771 0.000302771 0 0 0
13100 156.949 0 0 78.4744 135.918 0 0 0 334.824 0 0 0 0.000323079 0.000323079 0.000323079 0 0 0
13200 161.959 0 0 80.9793 140.256 0 0 0 345.512 0 0 0 6.0323e-05 6.0323e-05 6.0323e-05 0 0 0
13300 166.487 0 0 83.2434 144.178 0 0 0 355.172 0 0 0 0.000322086 0.000322086 0.000322086 0 0 0
13400 171.365 0 0 85.6825 148.402 0 0 0 365.579 0 0 0 0.000155041 0.000155041 0.000155041 0 0 0
13500 176.356 0 0 88.1782 152.725 0 0 0 376.227 0 0 0 0.000221984 0.000221984 0.000221984 0 0 0
13600 181.181 0 0 90.5905 156.903 0 0 0 386.52 0 0 0 0.000286023 0.000286023 0.000286023 0 0 0
13700 186.289 0 0 93.1444 161.326 0 0 0 397.416 0 0 0 0.000278626 0.000278626 0.000278626 0 0 0
13800 191.28 0 0 95.6402 165.649 0 0 0 408.065 0 0 0 0.000235454 0.000235454 0.000235454 0 0 0
13900 195.731 0 0 97.8656 169.503 0 0 0 417.56 0 0 0 0.000357376 0.000357376 0.000357376 0 0 0
14000 200.751 0 0 100.376 173.851 0 0 0 428.269 0 0 0 7.97252e-05 7.97252e-05 7.97252e-05 0 0 0
14100 206.083 0 0 103.042 178.468 0 0 0 439.644 0 0 0 0.000267319 0.000267319 0.000267319 0 0 0
14200 211.784 0 0 105.892 183.405 0 0 0 451.807 0 0 0 0.00028903 0.00028903 0.00028903 0 0 0
14300 217.602 0 0 108.801 188.443 0 0 0 464.218 0 0 0 0.000289943 0.000289943 0.000289943 0 0 0
14400 223.143 0 0 111.571 193.241 0 0 0 476.037 0 0 0 0.000304409 0.000304409 0.000304409 0 0 0
14500 228.37 0 0 114.185 197.769 0 0 0 487.19 0 0 0 0.000295061 0.000295061 0.000295061 0 0 0
14600 234.38 0 0 117.19 202.973 0 0 0 500.01 0 0 0 0.00028825 0.00028825 0.00028825 0 0 0
14700 240.382 0 0 120.191 208.171 0 0 0 512.816 0 0 0 0.000157154 0.000157154 0.000157154 0 0 0
14800 245.922 0 0 122.961 212.968 0 0 0 524.633 0 0 0 0.000130628 0.000130628 0.000130628 0 0 0
14900 251.241 0 0 125.621 217.575 0 0 0 535.981 0 0 0 1.05094e-05 1.05094e-05 1.05094e-05 0 0 0
15000 257.447 0 0 128.723 222.949 0 0 0 549.22 0 0 0 0.000224426 0.000224426 0.000224426 0 0 0
15100 262.981 0 0 131.491 227.742 0 0 0 561.027 0 0 0 0.000240168 0.000240168 0.000240168 0 0 0
15200 268.1 0 0 134.05 232.174 0 0 0 571.946 0 0 0 0.000209597 0.000209597 0.000209597 0 0 0
15300 273.768 0 0 136.884 237.083 0 0 0 584.039 0 0 0 7.12391e-05 7.12391e-05 7.12391e-05 0 0 0
15400 278.109 0 0 139.054 240.842 0 0 0 593.298 0 0 0 0.000129436 0.000129436 0.000129436 0 0 0
15500 283.327 0 0 141.663 245.361 0 0 0 604.43 0 0 0 0.000115671 0.000115671 0.000115671 0 0 0
15600 288.665 0 0 144.333 249.984 0 0 0 615.819 0 0 0 7.72233e-05 7.72233e-05 7.72233e-05 0 0 0
15700 293.574 0 0 146.787 254.235 0 0 0 626.292 0 0 0 0.000136041 0.000136041 0.000136041 0 0 0
15800 298.751 0 0 149.376 258.719 0 0 0 637.336 0 0 0 0.00018818 0.00018818 0.00018818 0 0 0
15900 304.308 0 0 152.154 263.531 0 0 0 649.191 0 0 0 0.00016774 0.00016774 0.00016774 0 0 0
16000 308.894 0 0 154.447 267.502 0 0 0 658.974 0 0 0 0.000168753 0.000168753 0.000168753 0 0 0
16100 313.262 0 0 156.631 271.285 0 0 0 668.291 0 0 0 8.92885e-05 8.92885e-05 8.92885e-05 0 0 0
16200 318.569 0 0 159.284 275.88 0 0 0 679.613 0 0 0 0.000270586 0.000270586 0.000270586 0 0 0
16300 324.551 0 0 162.275 281.061 0 0 0 692.375 0 0 0 0.000248017 0.000248017 0.000248017 0 0 0
16400 328.576 0 0 164.288 284.547 0 0 0 700.963 0 0 0 0.00012348 0.00012348 0.00012348 0 0 0
16500 332.075 0 0 166.038 287.577 0 0 0 708.427 0 0 0 3.03913e-05 3.03913e-05 3.03913e-05 0 0 0
16600 336.66 0 0 168.33 291.548 0 0 0 718.208 0 0 0 0.000178192 0.000178192 0.000178192 0 0 0
16700 340.581 0 0 170.291 294.943 0 0 0 726.573 0 0 0 0.000124396 0.000124396 0.000124396 0 0 0
16800 343.721 0 0 171.861 297.662 0 0 0 733.272 0 0 0 0.000217465 0.000217465 0.000217465 0 0 0
16900 348.951 0 0 174.476 302.192 0 0 0 744.429 0 0 0 0.000135973 0.000135973 0.000135973 0 0 0
17000 353.004 0 0 176.502 305.701 0 0 0 753.075 0 0 0 0.000151427 0.000151427 0.000151427 0 0 0
17100 357.801 0 0 178.9 309.856 0 0 0 763.308 0 0 0 9.7863e-05 9.7863e-05 9.7863e-05 0 0 0
17200 360.789 0 0 180.395 312.444 0 0 0 769.684 0 0 0 0.000164581 0.000164581 0.000164581 0 0 0
17300 364.588 0 0 182.294 315.733 0 0 0 777.788 0 0 0 0.000160363 0.000160363 0.000160363 0 0 0
17400 368.179 0 0 184.089 318.843 0 0 0 785.448 0 0 0 0.000141878 0.000141878 0.000141878 0 0 0
17500 372.535 0 0 186.268 322.616 0 0 0 794.742 0 0 0 0.000207809 0.000207809 0.000207809 0 0 0
17600 375.858 0 0 187.929 325.493 0 0 0 801.829 0 0 0 7.50523e-05 7.50523e-05 7.50523e-05 0 0 0
17700 378.699 0 0 189.35 327.953 0 0 0 807.891 0 0 0 9.50874e-05 9.50874e-05 9.50874e-05 0 0 0
17800 382.778 0 0 191.389 331.486 0 0 0 816.593 0 0 0 1.90819e-05 1.90819e-05 1.90819e-05 0 0 0
17900 385.272 0 0 192.636 333.646 0 0 0 821.914 0 0 0 0.000199801 0.000199801 0.000199801 0 0 0
18000 387.807 0 0 193.903 335.841 0 0 0 827.321 0 0 0 0.000106205 0.000106205 0.000106205 0 0 0
18100 390.536 0 0 195.268 338.204 0 0 0 833.143 0 0 0 8.01841e-05 8.01841e-05 8.01841e-05 0 0 0
18200 392.072 0 0 196.036 339.534 0 0 0 836.42 0 0 0 5.81394e-05 5.81394e-05 5.81394e-05 0 0 0
18300 395.761 0 0 197.881 342.729 0 0 0 844.291 0 0 0 4.23519e-06 4.23519e-06 4.23519e-06 0 0 0
18400 398.839 0 0 199.419 345.394 0 0 0 850.856 0 0 0 8.53081e-05 8.53081e-05 8.53081e-05 0 0 0
18500 400.997 0 0 200.498 347.263 0 0 0 855.46 0 0 0 0.000177918 0.000177918 0.000177918 0 0 0
18600 403.623 0 0 201.811 349.537 0 0 0 861.062 0 0 0 2.82167e-05 2.82167e-05 2.82167e-05 0 0 0
18700 405.933 0 0 202.967 351.538 0 0 0 865.991 0 0 0 5.07139e-05 5.07139e-05 5.07139e-05 0 0 0
18800 407.614 0 0 203.807 352.994 0 0 0 869.577 0 0 0 -7.98805e-05 -7.98805e-05 -7.98805e-05 0 0 0
18900 409.739 0 0 204.869 354.834 0 0 0 874.109 0 0 0 -8.27189e-05 -8.27189e-05 -8.27189e-05 0 0 0
19000 413.15 0 0 206.575 357.788 0 0 0 881.387 0 0 0 7.53085e-05 7.53085e-05 7.53085e-05 0 0 0
19100 415.78 0 0 207.89 360.065 0 0 0 886.997 0 0 0 8.3559e-05 8.3559e-05 8.3559e-05 0 0 0
19200 418.985 0 0 209.493 362.841 0 0 0 893.835 0 0 0 -2.55831e-05 -2.55831e-05 -2.55831e-05 0 0 0
19300 420.105 0 0 210.052 363.811 0 0 0 896.224 0 0 0 0.000113151 0.000113151 0.000113151 0 0 0
19400 421.834 0 0 210.917 365.308 0 0 0 899.912 0 0 0 2.81355e-05 2.81355e-05 2.81355e-05 0 0 0
19500 423.815 0 0 211.907 367.023 0 0 0 904.138 0 0 0 0.000121987 0.000121987 0.000121987 0 0 0
19600 426.728 0 0 213.364 369.546 0 0 0 910.353 0 0 0 1.19396e-05 1.19396e-05 1.19396e-05 0 0 0
19700 427.268 0 0 213.634 370.014 0 0 0 911.505 0 0 0 -9.72912e-06 -9.72912e-06 -9.72912e-06 0 0 0
19800 427.932 0 0 213.966 370.589 0 0 0 912.922 0 0 0 -3.32493e-05 -3.32493e-05 -3.32493e-05 0 0 0
19900 430.625 0 0 215.312 372.921 0 0 0 918.666 0 0 0 -1.32204e-05 -1.32204e-05 -1.32204e-05 0 0 0
20000 430.873 0 0 215.436 373.136 0 0 0 919.195 0 0 0 -5.17465e-05 -5.17465e-05 -5.17465e-05 0 0 0
structure grama.psf
coordinates grama.pdb
temperature 0
parameters par_all27_prot_lipid.inp
parameters par-extraterms.inp
paraTypeCharmm on
outputEnergies 10
outputTiming 100
xstFreq 100
dcdFreq 100
wrapAll on
wrapNearest on
timestep 1
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 20
switching on
switchDist 8.5
cutoff 10
pairlistdist 11.5
cellBasisVector1 30.00 00.00 00.00
cellBasisVector2 15.00 25.98 00.00
cellBasisVector3 00.00 00.00 64.00
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 10
Pme on
PmeGridsizeX 32
PmeGridsizeY 32
PmeGridsizeZ 64
exclude scaled1-4
1-4scaling 1.0
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile fix_backbone.pdb
fixedAtomsCol B
constraints on
consRef restrain_ca.pdb
consKFile restrain_ca.pdb
consKCol B
langevin on
langevinDamping 10
langevinTemp 310
langevinHydrogen no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310
useGroupPressure yes # smaller fluctuations
useFlexibleCell no # allow dimensions to fluctuate independently
useConstantRatio no # fix shape in x-y plane
binaryoutput off
outputname equil_out
# run one step to get into scripting mode
minimize 0
# turn off until later
langevinPiston off
# minimize nonbackbone atoms
minimize 1000
output min_fix
# min all atoms
fixedAtoms off
minimize 1000
output min_all
# heat with CAs restrained
#langevin on
run 3000
output heat
# equilibrate volume with CAs restrained
langevinPiston on
run 5000
output equil_ca
# equilibrate volume without restraints
constraintScaling 0
run 10000
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:45 CST