Thank you.<br><br>First, I confirmed the broken lipid with ngmx.<br><br>I did "pbc = xyz", and I downloaded the "popc.itp" from Dr. Tieleman's homepage.<br>[ bonds ] section in "popc.itp" is okay.
<br>Running MD is okay. (It doesn't crash; no extreme velocity)<br><br>It's strange that some lipids around the boundary are kept in whole molecules,<br>but some are not.<br><br><br><br><br><div class="gmail_quote">
On Jan 15, 2008 12:37 PM, 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;">Try using ngmx to visualise the simulation like I said, that'll tell you exactly what bonds gromacs thinks are there and definitively confirm whether there's a problem in the setup.
</div>
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">Files that may have caused the problem are of course the obvious things like your mdp (what you've set pbc to, for instance), your topology (have you specified the bonds correctly in the first place?).
<br>If it turns out to just be a visualisation problem when using VMD, try using trjconv to dump out the first frame directly as a .gro for VMD. And, of course, using trjconv and specifying an appropriate -pbc option to 'fix' the pbc is something to do.
<br></div>
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;"><div class="Ih2E3d">----- 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></div><div><div></div><div class="Wj3C7c">Sent: Tuesday, January 15, 2008 5:18:58 PM
<br>Subject: Re: [gmx-users] image control<br><br>I don't think this is caused by VMD.<br>The real coordinates of the part of the molicule in the .gro file (restart file from the end of simulation) will tell you.<br>This means gromacs doesn't keep the whole molecule.
<br><br>Would you let me know what simulation setup you need for the cheking?<br><br>I used editconf to convert the .pdb file to .gro file.<br>Since the structure (.pdb) was pre-equilibrated one, I did setup box size manually (not using editconf).
<br>There were more than three float numbers at the bottom of .gro file.<br>I left only the first three, and replaced with the known box size.<br><br>Is this enough for PBC
simulation? (manually typing box size at the bottom of .gro file) <br><br><br>
<div class="gmail_quote">On Jan 15, 2008 10:13 AM, Alan Dodd <<a href="mailto:anoddlad@yahoo.com" rel="nofollow" target="_blank">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;">
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<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">I'd suggest this is an issue with VMD rather than gromacs. You have to be quite careful which .gro you use to provide the original structure, make sure it is actually the starting frame and not anything else - this is something I've seen cause this sort of problem before.
</div>
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">Normally, of course, PBC settings in Gromacs keep molecules whole in the output file quite reliably, but not knowing how you've set your simulation up, I couldn't comment on that. Using ngmx is a good way to check that Gromacs itself is doing what you think it is.
<br><br></div>
<div style="font-size: 12pt; font-family: times new roman,new york,times,serif;">
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<div></div>
<div>----- Original Message ----<br>From: Myunggi Yi <<a href="mailto:myunggi@gmail.com" rel="nofollow" target="_blank"> myunggi@gmail.com</a>><br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" rel="nofollow" target="_blank">
gmx-users@gromacs.org</a>><br>Sent: Tuesday, January 15, 2008 2:51:20 PM<br>Subject: [gmx-users] image control <br><br>Dear users,<br><br>I'm running NPT simulation POPC with a short peptide.<br>I see the long bonds across the unit cell in VMD.
<br>Why am I getting broken lipid molecules in the trajectory (original .xtc file w/o any post-modification)? <br><br>Some lipids move whole molecules, but some are broken.<br>How can I control the unit of image?<br>I couldn't find any related word in the manual.
<br><br>I assume image will be done by "residue".<br>Then I shouldn't get this strange result. <br><br>I got the
popc.itp from Dr. Tieleman's web site.<br>Any idea?<br><br clear="all"><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">http://www.scs.fsu.edu/~myunggi</a> </div></div>
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