[gmx-users] T-coupling of water and ion
Jian Zou
zouj01 at mails.tsinghua.edu.cn
Wed Jun 1 03:58:32 CEST 2005
Hi Anton,
Thanks for your comments.
Anton Feenstra wrote:
> And which ref_t did you use during PR-MD?
400K, too.
> Your *whole* system is (far) below the 400K ref_t. I can't see how your
> mdp file could have produced these results. Are you sure these are the
> settings you used? Perhaps you can check your .tpr file or md.log (or
> md0.log)?
I use g_energy to generate the temperature again, using
> g_energy -f md_ener.edr -o T-ener.xvg
and choose
Temperature, T-RNA, T-SOL, T-Na
the results are as follows
####
# time Temperature T-RNA T-SOL T-Na
####
0.000000 394.552277 396.710052 394.425232 261.817810
2.000000 401.028137 390.325897 401.582977 243.876129
4.000000 402.511139 411.360046 402.510193 337.482910
6.000000 398.780670 425.899078 398.483795 407.033661
8.000000 397.275269 386.858276 397.842712 336.869507
10.000000 401.389954 394.441925 401.492096 403.169098
12.000001 401.387543 413.248230 401.677216 318.522461
14.000001 401.661621 384.849396 401.963745 360.555786
16.000000 398.779480 437.932556 398.529877 407.255005
18.000000 401.597931 398.320709 401.597687 454.932404
20.000000 398.766449 413.073578 398.662567 526.835938
22.000002 400.371796 422.870758 400.196625 428.220886
24.000002 398.436859 425.191895 398.186646 351.420105
26.000002 402.825714 396.661926 402.748291 419.390106
28.000002 400.630585 378.204620 400.718262 287.050079
30.000002 401.466339 351.022797 401.962494 346.846375
32.000000 398.274902 402.642059 398.128937 317.049927
34.000000 398.028687 369.139313 398.261719 386.328735
36.000000 403.275055 406.268799 403.597931 398.076477
38.000000 397.202393 402.614838 397.375366 363.127686
40.000000 397.545502 380.705750 397.695618 316.021271
42.000004 401.520569 404.314453 401.245422 617.735413
44.000004 399.144653 383.625031 399.169403 634.819641
46.000004 399.720062 389.394897 399.640076 367.592316
48.000004 400.529175 370.691437 400.998718 317.573700
50.000004 397.023071 392.908936 397.175751 406.068085
52.000004 398.431549 403.980408 398.486755 389.311737
54.000004 402.674225 425.877502 402.659760 389.169220
56.000004 400.456421 366.853760 400.655121 499.275299
58.000004 400.842590 399.351105 400.982605 371.754730
60.000004 402.830200 415.674744 402.555634 542.111877
62.000004 396.353912 391.834595 396.492218 333.349976
64.000000 396.784912 366.488647 397.424561 304.118500
66.000000 399.008453 421.069092 398.908386 318.676056
68.000000 403.005524 394.880157 402.833435 508.849823
70.000000 400.397278 410.545929 400.315765 229.863907
72.000000 399.931061 416.443115 399.848389 417.084167
74.000000 401.220795 389.778351 401.157532 387.723236
76.000000 399.620178 383.638763 399.891632 251.903427
78.000000 399.302490 443.134705 398.746613 468.050110
80.000000 403.261292 416.147766 403.383179 443.099579
82.000008 399.208984 415.098694 398.723511 430.627380
84.000008 398.675293 404.318115 398.684875 377.655792
86.000008 399.872131 407.730347 399.563812 634.604309
88.000008 399.121674 448.161652 398.967529 525.212952
90.000008 397.943390 366.419983 397.992340 372.959656
92.000008 402.746277 452.841736 402.045471 484.276520
94.000008 401.128967 389.797546 401.317535 394.251038
96.000008 402.745697 433.749634 402.401733 405.763702
98.000008 400.094452 398.284027 400.157227 575.691406
100.000008 400.617310 386.067078 400.712189 436.440491
102.000008 398.434967 434.999939 397.848328 731.976318
104.000008 399.477386 435.381500 398.889557 403.400452
106.000008 395.172455 381.178284 395.335907 455.880280
108.000008 399.337372 362.908081 399.610504 636.233276
110.000008 401.230652 454.067841 400.617981 402.470306
112.000008 398.314972 391.495728 398.373016 395.224426
114.000008 399.211029 389.503662 399.375244 396.406586
116.000008 400.976654 399.594574 401.128998 273.305664
118.000008 399.282074 403.354370 399.176392 340.471222
120.000008 402.661591 424.447693 402.466400 301.303558
122.000008 401.606476 408.250000 401.707733 220.067490
124.000008 397.631897 385.387787 397.931946 291.533356
126.000008 398.900543 379.361694 398.888458 565.851929
128.000000 398.749908 371.992584 399.282623 334.573212
130.000000 398.406006 383.545807 398.292664 538.234741
132.000000 398.763458 396.139282 398.980682 301.829193
134.000000 398.420929 362.606354 398.658295 346.085266
136.000000 398.450623 390.521332 398.489136 331.876038
138.000000 400.417511 394.661377 400.441162 434.250793
140.000000 402.894501 367.212036 403.126068 262.448059
142.000000 398.258179 401.157623 398.187805 334.663544
144.000000 399.731964 376.687744 399.734039 420.562317
146.000000 401.122101 434.914215 400.952209 393.306030
148.000000 403.701843 395.841736 404.029114 411.973572
150.000000 399.684784 389.992706 399.668335 325.147278
152.000000 399.031372 401.726105 399.240936 429.877991
154.000000 399.390564 437.711975 398.798248 626.526489
156.000000 402.882050 386.321136 403.400177 300.558807
158.000000 397.923737 406.974548 397.776337 418.947205
160.000000 403.346375 404.880676 403.445953 379.397797
162.000015 401.868774 423.087067 401.614777 344.789795
164.000015 398.602722 464.861603 397.868347 475.204285
166.000015 398.470001 435.760010 398.177002 338.957306
168.000015 398.106689 358.039978 398.346863 499.818390
170.000015 404.164154 391.614807 404.384979 402.603119
172.000015 398.914429 395.423065 398.666748 503.441986
174.000015 400.707092 398.534149 400.792877 397.761963
176.000015 398.871246 392.972290 398.941589 388.148682
178.000015 402.635498 419.853058 402.550934 286.817719
180.000015 398.778717 404.821014 398.871246 341.052765
182.000015 395.440735 399.093353 395.639679 356.743347
184.000015 399.931915 412.938721 399.732574 402.136047
186.000015 397.331085 406.106293 397.321228 420.079071
188.000015 397.279907 406.930725 397.362000 445.048645
190.000015 400.357635 330.934052 401.095123 237.431183
192.000015 400.440857 396.785583 400.386200 398.665649
194.000015 403.284424 403.035431 403.349731 369.567841
196.000015 399.205200 394.442719 399.109467 513.191589
198.000015 398.144775 397.296967 398.176331 509.243805
200.000015 400.778656 388.481903 400.895599 348.153351
This time, the above result is likely to be what I want.
I don't know why the g_energy results from ener.edr is so different from the
g_traj results from the trr file.
how to understand the difference?
I forgot to state that I also add afm_pulling on the RNA segment, for I did
simulations under constaint=no dt=1fs before (other conditions the same).
This should add up to the translational kinetic energy, which may affect
Temperature as well.
Did I miss something?
Thank you so much for your advice and comment!
Regards,
Jian Zou
More information about the gromacs.org_gmx-users
mailing list