Thank you all of you.<br><br>I've got a pre-equilibrated hydrated POPC bilayer from a web-site.<br>I made a hole, and I placed my protein.<br>Now, what is the next step?<br><br><br><div class="gmail_quote">On Jan 15, 2008 4:58 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><div></div><div class="Wj3C7c">
Quoting Myunggi Yi <<a href="mailto:myunggi@gmail.com">myunggi@gmail.com</a>>:<br><br>> On Jan 15, 2008 2:48 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>><br>> > 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<br>
> > (restart<br>> > > file from the end of simulation) will tell you.<br>> > > This means gromacs doesn't keep the whole molecule.<br>> ><br>> > I have never known mdrun to write a broken molecule, so I would suspect
<br>> > the<br>> > visualization as well.<br>> ><br>><br>> As I said I have already confirmed with ngmx, and I can check<br>> the .gro file (text file).<br>><br>><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>> > What .pdb structure? Your statement above said you already had a .gro<br>> > file.<br>> ><br>
><br>> I did the initial setup from pre-equilibrated pdb file.<br>> Then the above (.gro) is the MD result.<br>><br>><br>> > > Since the structure (.pdb) was pre-equilibrated one, I did setup box<br>
> > size<br>> > > manually (not using editconf).<br>> ><br>> > Why not? Using editconf should produce the appropriate box dimensions at<br>> > the<br>> > bottom of the output .gro file.
<br>> ><br>><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<br>> be distorted a lot.<br><br></div>
</div>Perhaps I'm missing the purpose of what you're trying to do. Do I understand<br>correctly that you have a pre-equilibrated system (.pdb) and you want to run MD<br>on a similar system that is just larger? To me, that sounds like a job for
<br>genconf with the original .pdb file (create replicas of your system with an<br>appropriate box size, not one that gets put in manually).<br><br>If I'm misunderstanding, it might be beneficial to describe your system in a bit
<br>more detail so we can all understand what's going on.<br><div class="Ih2E3d"><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><br></div>See above, regarding genconf, if that's what you're trying to do.<br><font color="#888888"><br>-Justin<br>
</font><div><div></div><div class="Wj3C7c"><br>><br>><br>> ><br>> > -Justin<br>> ><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<br>> > 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<br>> > to be<br>> > > > quite careful which .gro you use to provide the original structure,
<br>> > 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
<br>> > the<br>> > > > output file quite reliably, but not knowing how you've set your<br>> > simulation<br>> > > > up, I couldn't comment on that. Using ngmx is a good way to check
<br>> > 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<br>> > .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
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<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> <<a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">http://www.scs.fsu.edu/%7Emyunggi</a>><br>> > >
<br>> ><br>> ><br>> ><br></div></div><div><div></div><div class="Wj3C7c">> > ========================================<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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</a><br>> ><br>><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" target="_blank">http://www.scs.fsu.edu/~myunggi</a><br>><br><br><br><br>========================================
<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><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>