[gmx-users] Regarding Box-X Box-Y values from g_energy

Sona Aramyan sona_aramyan at yahoo.com
Thu Nov 1 16:11:56 CET 2007


Thank you very much for your suggestion.
I've checked out. I've used isotropic  pressure
coupling.
If anyone has more suggestion please share with me.

--- Alan Dodd <anoddlad at yahoo.com> wrote:

> Did you perhaps use semiisotropic pressure coupling?
>  I'd expect the X-Y values to be the same for that.
> 
> ----- Original Message ----
> From: Sona Aramyan <sona_aramyan at yahoo.com>
> To: Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Sent: Thursday, November 1, 2007 1:18:07 PM
> Subject: [gmx-users] Regarding Box-X Box-Y values
> from g_energy
> 
> Dear gmx-users
> 
> 
> I have a system consisting from 128dppc bilayer
> which
> I've took from 
>
http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies)
> and 1 molecule of DALA. I have 2ns run of it. In my
> g_energy output energy.xvg, in which I have Box-X
> Box-Y Box-Z values, the values of Box-X and  Box-Y
> at
> every step of time have exactly same values.
> 
> How can this two values change with the same
> quantity?
> 
> Is this a real problem, can I use the results of the
> it or something is wrong with this simulation? 
> 
> I'm sending to you a part of my energy.xvg
> 
> Any suggestions and advises will be very very
> appreciated.
> 
> 
> 
> # This file was created by g_energy
> # which is part of G R O M A C S:
> # Gnomes, ROck Monsters And Chili Sauce
> # All this happened at: Thu Oct 25 15:12:53 2007
> #
> @    title "Gromacs Energies"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "E (kJ mol\S-1\N)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Box-X"
> @ s1 legend "Box-Y"
> @ s2 legend "Box-Z"
>     0.000000    6.343720    6.343720    6.777830
>     4.000000    6.279631    6.279631    6.709337
>     8.000000    6.246550    6.246550    6.673972
>   12.000001    6.291696    6.291696    6.722235
>   16.000000    6.274485    6.274485    6.703831
>   20.000000    6.259673    6.259673    6.688022
>   24.000002    6.274458    6.274458    6.703805
>   28.000002    6.269053    6.269053    6.698055
>   32.000000    6.273066    6.273066    6.702339
>   36.000000    6.277720    6.277720    6.707294
>   40.000000    6.268405    6.268405    6.697363
>   44.000004    6.262165    6.262165    6.690718
>   48.000004    6.271516    6.271516    6.700673
>   52.000004    6.282900    6.282900    6.712825
>   56.000004    6.268004    6.268004    6.696920
>   60.000004    6.275951    6.275951    6.705416
>   64.000000    6.283990    6.283990    6.713978
>   68.000000    6.268332    6.268332    6.697258
>   72.000000    6.268672    6.268672    6.697591
>   76.000000    6.282032    6.282032    6.711858
>   80.000000    6.275910    6.275910    6.705327
>   84.000008    6.271963    6.271963    6.701087
>   88.000008    6.271978    6.271978    6.701059
>   92.000008    6.265982    6.265982    6.694634
>   96.000008    6.272739    6.272739    6.701852
>   100.000008    6.270991    6.270991    6.699977
>   104.000008    6.259323    6.259323    6.687513
>   108.000008    6.265584    6.265584    6.694173
>   112.000008    6.269279    6.269279    6.698182
>   116.000008    6.267590    6.267590    6.696383
>   120.000008    6.266372    6.266372    6.695080
>   124.000008    6.257270    6.257270    6.685329
>   128.000000    6.263762    6.263762    6.692231
>   132.000000    6.272191    6.272191    6.701218
>   136.000000    6.266236    6.266236    6.694935
>   140.000000    6.261252    6.261252    6.689645
>   144.000000    6.259418    6.259418    6.687694
>   148.000000    6.268799    6.268799    6.697742
>   152.000000    6.274210    6.274210    6.703519
>   156.000000    6.269886    6.269886    6.698938
>   160.000000    6.273304    6.273304    6.702565
>   164.000015    6.270255    6.270255    6.699334
>   168.000015    6.279771    6.279771    6.709496
>   172.000015    6.271050    6.271050    6.700203
>   176.000015    6.258578    6.258578    6.686853
>   180.000015    6.269828    6.269828    6.698884
>   184.000015    6.276379    6.276379    6.705905
>   188.000015    6.260080    6.260080    6.688455
>   192.000015    6.261606    6.261606    6.690063
>   196.000015    6.275762    6.275762    6.705174
>   200.000015    6.263684    6.263684    6.692267
> 
> 
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