I didn't do any conversion. The gro file is restart file of the end of MD.<br><br><div class="gmail_quote">On Jan 15, 2008 4:18 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.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;">Hi Myunggi Yi,<br><br>Did you by chance use trjconv prior to visualization? If so, what options did you use? mdrun doesn't write broken molecules.
<br><br>Cheers,<br><br>Tsjerk<div><div></div><div class="Wj3C7c"><br><br><div class="gmail_quote">On Jan 15, 2008 8:48 PM, Justin A. Lemkul <
<a href="mailto:jalemkul@vt.edu" target="_blank">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>Quoting Myunggi Yi <
<a href="mailto:myunggi@gmail.com" target="_blank">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><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><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><br>-Justin<br><div><div></div><div><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" target="_blank">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" 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, 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>> ><br>> ><br>> > -----Inline Attachment Follows-----<br>> ><br>
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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" target="_blank">jalemkul@vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/" target="_blank">
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/</a><br><br>========================================<br><div><div></div><div>_______________________________________________<br>gmx-users mailing list
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<br clear="all"><br></div></div>-- <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
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</a><br></blockquote></div><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/~myunggi">http://www.scs.fsu.edu/~myunggi</a>