[gmx-users] Regarding Box-X Box-Y values from g_energy
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Nov 1 20:26:25 CET 2007
Hi Sona,
If you use isotropic pressure coupling, there will be a single scaling
factor for all three dimensions. So if the box lengths are equal at the
start, they will always remain equal.
Best,
Tsjerk
On 11/1/07, Sona Aramyan <sona_aramyan at yahoo.com> wrote:
>
> 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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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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