I didn't do any conversion. The gro file is restart file of the end of MD. On Jan 15, 2008 4:18 PM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Myunggi Yi, > > Did you by chance use trjconv prior to visualization? If so, what options > did you use? mdrun doesn't write broken molecules. > > Cheers, > > Tsjerk > > > On Jan 15, 2008 8:48 PM, Justin A. Lemkul < [EMAIL PROTECTED]> wrote: > > > 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>< > > 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 <http://www.scs.fsu.edu/%7Emyunggi> > > > > > > > > > > > ======================================== > > > > 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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > Junior UD (post-doc) > Biomolecular NMR, Bijvoet Center > Utrecht University > Padualaan 8 > 3584 CH Utrecht > The Netherlands > P: +31-30-2539931 > F: +31-30-2537623 > _______________________________________________ > 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
_______________________________________________ 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
