Thank you for the reply.<br><br>I did center only, but I didn't see much difference from the original structure.<br>Since the solvent is separated, centering cannot do much.<br><br>I decided to translate the whole system to shift up (out of box),
<br>and then to move it back to the unit cell.<br>However, this "shift" doesn't work at all.<br>The output is exactly same as the original.<br><br>I may need the "framenr".<br><br> -shift vector 0 0 0 All coordinates will be shifted by framenr*shift
<br><br>This "help" message doesn't help me at all. I have no idea.<br><br>I changed my mind.<br>Since the "center" option gives me the translated structure,<br>I picked an atom to shift the system.
<br><br>Now I can move the atoms outside box to the unit cell using -pbc option,<br>however, all options give me the broken molecules.<br><br>How can I solve this problem?<br><br>Happy holidays.<br><br><br><div class="gmail_quote">
On Dec 26, 2007 5:40 AM, Alan Dodd <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">Have you tried running trjconv with -centre (selecting SOL, obviously), and then running trjconv -pbc on the result? I have a vague memory of finding seperating the commands gives a different result, as if the two options were interfering with each other. What does the output look like when you use the option -centre? If nothing else, seperating the commands might help you find the source of the problem.
<br><br>
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;"><div><div></div><div class="Wj3C7c">----- Original Message ----<br>From: Myunggi Yi <<a href="mailto:myunggi@gmail.com" target="_blank">
myunggi@gmail.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Sent: Tuesday, December 25, 2007 9:48:29 PM<br>Subject: [gmx-users] image centering
<br><br>Dear users,<br><br>I have a membrane simulation trajectory,<br>in which the solvent (water and ions) is separated by lipid bilayer.<br><br>I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell.
<br><br>I have tried the followings.<br><br>trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster<br>trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx -center rect -pbc whole<br clear="all">
<br>Both pbc and center didn't work.<br>Is there any way to center the solvent?<br><br>Happy holidays.<br><br><br>-- <br>Best wishes,<br><br>MYUNGGI
YI<br>==================================<br>KLB 419<br>Institute of Molecular Biophysics <br>Florida State University<br>Tallahassee, FL 32306<br><br>Office: (850) 645-1334<br><a href="http://www.scs.fsu.edu/%7Emyunggi" rel="nofollow" target="_blank">
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