[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




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