Hi Sona,<br><br>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.<br><br>Best,<br><br>Tsjerk
<br><br><div><span class="gmail_quote">On 11/1/07, <b class="gmail_sendername">Sona Aramyan</b> <<a href="mailto:sona_aramyan@yahoo.com">sona_aramyan@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you very much for your suggestion.<br>I've checked out. I've used isotropic pressure<br>coupling.<br>If anyone has more suggestion please share with me.<br><br>--- Alan Dodd <<a href="mailto:anoddlad@yahoo.com">
anoddlad@yahoo.com</a>> wrote:<br><br>> Did you perhaps use semiisotropic pressure coupling?<br>> I'd expect the X-Y values to be the same for that.<br>><br>> ----- Original Message ----<br>> From: Sona Aramyan <
<a href="mailto:sona_aramyan@yahoo.com">sona_aramyan@yahoo.com</a>><br>> To: Discussion list for GROMACS users<br>> <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Thursday, November 1, 2007 1:18:07 PM
<br>> Subject: [gmx-users] Regarding Box-X Box-Y values<br>> from g_energy<br>><br>> Dear gmx-users<br>><br>><br>> I have a system consisting from 128dppc bilayer<br>> which<br>> I've took from
<br>><br><a href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</a>)<br>> and 1 molecule of DALA. I have 2ns run of it. In my
<br>> g_energy output energy.xvg, in which I have Box-X<br>> Box-Y Box-Z values, the values of Box-X and Box-Y<br>> at<br>> every step of time have exactly same values.<br>><br>> How can this two values change with the same
<br>> quantity?<br>><br>> Is this a real problem, can I use the results of the<br>> it or something is wrong with this simulation?<br>><br>> I'm sending to you a part of my energy.xvg<br>><br>> Any suggestions and advises will be very very
<br>> appreciated.<br>><br>><br>><br>> # This file was created by g_energy<br>> # which is part of G R O M A C S:<br>> # Gnomes, ROck Monsters And Chili Sauce<br>> # All this happened at: Thu Oct 25 15:12:53 2007
<br>> #<br>> @ title "Gromacs Energies"<br>> @ xaxis label "Time (ps)"<br>> @ yaxis label "E (kJ mol\S-1\N)"<br>> @TYPE xy<br>> @ view 0.15, 0.15, 0.75, 0.85<br>> @ legend on
<br>> @ legend box on<br>> @ legend loctype view<br>> @ legend 0.78, 0.8<br>> @ legend length 2<br>> @ s0 legend "Box-X"<br>> @ s1 legend "Box-Y"<br>> @ s2 legend "Box-Z"
<br>> 0.000000 6.343720 6.343720 6.777830<br>> 4.000000 6.279631 6.279631 6.709337<br>> 8.000000 6.246550 6.246550 6.673972<br>> 12.000001 6.291696 6.291696 6.722235
<br>> 16.000000 6.274485 6.274485 6.703831<br>> 20.000000 6.259673 6.259673 6.688022<br>> 24.000002 6.274458 6.274458 6.703805<br>> 28.000002 6.269053 6.269053 6.698055
<br>> 32.000000 6.273066 6.273066 6.702339<br>> 36.000000 6.277720 6.277720 6.707294<br>> 40.000000 6.268405 6.268405 6.697363<br>> 44.000004 6.262165 6.262165 6.690718
<br>> 48.000004 6.271516 6.271516 6.700673<br>> 52.000004 6.282900 6.282900 6.712825<br>> 56.000004 6.268004 6.268004 6.696920<br>> 60.000004 6.275951 6.275951 6.705416
<br>> 64.000000 6.283990 6.283990 6.713978<br>> 68.000000 6.268332 6.268332 6.697258<br>> 72.000000 6.268672 6.268672 6.697591<br>> 76.000000 6.282032 6.282032 6.711858
<br>> 80.000000 6.275910 6.275910 6.705327<br>> 84.000008 6.271963 6.271963 6.701087<br>> 88.000008 6.271978 6.271978 6.701059<br>> 92.000008 6.265982 6.265982 6.694634
<br>> 96.000008 6.272739 6.272739 6.701852<br>> 100.000008 6.270991 6.270991 6.699977<br>> 104.000008 6.259323 6.259323 6.687513<br>> 108.000008 6.265584 6.265584 6.694173
<br>> 112.000008 6.269279 6.269279 6.698182<br>> 116.000008 6.267590 6.267590 6.696383<br>> 120.000008 6.266372 6.266372 6.695080<br>> 124.000008 6.257270 6.257270 6.685329
<br>> 128.000000 6.263762 6.263762 6.692231<br>> 132.000000 6.272191 6.272191 6.701218<br>> 136.000000 6.266236 6.266236 6.694935<br>> 140.000000 6.261252 6.261252 6.689645
<br>> 144.000000 6.259418 6.259418 6.687694<br>> 148.000000 6.268799 6.268799 6.697742<br>> 152.000000 6.274210 6.274210 6.703519<br>> 156.000000 6.269886 6.269886 6.698938
<br>> 160.000000 6.273304 6.273304 6.702565<br>> 164.000015 6.270255 6.270255 6.699334<br>> 168.000015 6.279771 6.279771 6.709496<br>> 172.000015 6.271050 6.271050 6.700203
<br>> 176.000015 6.258578 6.258578 6.686853<br>> 180.000015 6.269828 6.269828 6.698884<br>> 184.000015 6.276379 6.276379 6.705905<br>> 188.000015 6.260080 6.260080 6.688455
<br>> 192.000015 6.261606 6.261606 6.690063<br>> 196.000015 6.275762 6.275762 6.705174<br>> 200.000015 6.263684 6.263684 6.692267<br>><br>><br>> __________________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
P: +31-30-2539931 <br>F: +31-30-2537623