Quoting Myunggi Yi <[EMAIL PROTECTED]>: > I don't think this is caused by VMD. > The real coordinates of the part of the molicule in the .gro file (restart > file from the end of simulation) will tell you. > This means gromacs doesn't keep the whole molecule.
I have never known mdrun to write a broken molecule, so I would suspect the visualization as well. > > Would you let me know what simulation setup you need for the cheking? > > I used editconf to convert the .pdb file to .gro file. What .pdb structure? Your statement above said you already had a .gro file. > Since the structure (.pdb) was pre-equilibrated one, I did setup box size > manually (not using editconf). Why not? Using editconf should produce the appropriate box dimensions at the bottom of the output .gro file. -Justin > There were more than three float numbers at the bottom of .gro file. > I left only the first three, and replaced with the known box size. > > Is this enough for PBC simulation? (manually typing box size at the bottom > of .gro file) > > > On Jan 15, 2008 10:13 AM, Alan Dodd <[EMAIL PROTECTED]> wrote: > > > 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. > > 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. > > > > ----- Original Message ---- > > From: Myunggi Yi <[EMAIL PROTECTED]> > > To: Discussion list for GROMACS users <[email protected]> > > Sent: Tuesday, January 15, 2008 2:51:20 PM > > Subject: [gmx-users] image control > > > > Dear users, > > > > I'm running NPT simulation POPC with a short peptide. > > I see the long bonds across the unit cell in VMD. > > Why am I getting broken lipid molecules in the trajectory (original .xtc > > file w/o any post-modification)? > > > > Some lipids move whole molecules, but some are broken. > > How can I control the unit of image? > > I couldn't find any related word in the manual. > > > > I assume image will be done by "residue". > > Then I shouldn't get this strange result. > > > > I got the popc.itp from Dr. Tieleman's web site. > > Any idea? > > > > > > -- > > Best wishes, > > > > MYUNGGI YI > > ================================== > > KLB 419 > > Institute of Molecular Biophysics > > Florida State University > > Tallahassee, FL 32306 > > > > Office: (850) 645-1334 > > http://www.scs.fsu.edu/~myunggi <http://www.scs.fsu.edu/%7Emyunggi> > > > > > > -----Inline Attachment Follows----- > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > ------------------------------ > > Never miss a thing. Make Yahoo your > homepage.<http://us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Best wishes, > > MYUNGGI YI > ================================== > KLB 419 > Institute of Molecular Biophysics > Florida State University > Tallahassee, FL 32306 > > Office: (850) 645-1334 > http://www.scs.fsu.edu/~myunggi > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
