<br><br><div class="gmail_quote">On Jan 15, 2008 2:48 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="Ih2E3d">Quoting Myunggi Yi <<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>>:<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
<br>> file from the end of simulation) will tell you.<br>> This means gromacs doesn't keep the whole molecule.<br><br></div>I have never known mdrun to write a broken molecule, so I would suspect the<br>visualization as well.
<br><div class="Ih2E3d"></div></blockquote><div><br>As I said I have already confirmed with ngmx, and I can check <br>the .gro file (text file).<br><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><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><br></div>What .pdb structure? Your statement above said you already had a .gro file.
<br><div class="Ih2E3d"></div></blockquote><div><br>I did the initial setup from pre-equilibrated pdb file. <br>Then the above (.gro) is the MD result.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>> Since the structure (.pdb) was pre-equilibrated one, I did setup box size<br>> manually (not using editconf).<br><br></div>Why not? Using editconf should produce the appropriate box dimensions at the
<br>bottom of the output .gro file.<br></blockquote><div><br>Since I have pre-equilibrated system, I don't want to waste time.<br>As you know If I make a large box, during the equilibration the system will be distorted a lot.
<br>To get the right system I need long long time equilibration.<br><br>However, my question is this.<br>Does this cause the image problem?<br>Even though I prepare the large BOX with "editconf", I see the same problem.
<br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>-Justin<br><div><div></div><div class="Wj3C7c"><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<br>> of .gro file)<br>><br>><br>> On Jan 15, 2008 10:13 AM, Alan Dodd <
<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:<br>><br>> > I'd suggest this is an issue with VMD rather than gromacs. You have to be<br>> > quite careful which .gro you use to provide the original structure, make
<br>> > sure it is actually the starting frame and not anything else - this is<br>> > something I've seen cause this sort of problem before.<br>> > Normally, of course, PBC settings in Gromacs keep molecules whole in the
<br>> > output file quite reliably, but not knowing how you've set your simulation<br>> > up, I couldn't comment on that. Using ngmx is a good way to check that<br>> > Gromacs itself is doing what you think it is.
<br>> ><br>> > ----- Original Message ----<br>> > From: Myunggi Yi <<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>><br>> > To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">
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<br>> > 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>> ><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></div></div>> > <a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">
http://www.scs.fsu.edu/~myunggi</a> <<a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">http://www.scs.fsu.edu/%7Emyunggi</a>><br><div class="Ih2E3d">> ><br>> ><br>> > -----Inline Attachment Follows-----
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<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" target="_blank">http://www.scs.fsu.edu/~myunggi</a><br>><br><br><br><br></div>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant
<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">
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<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/~myunggi">http://www.scs.fsu.edu/~myunggi</a>