Thank you. First, I confirmed the broken lipid with ngmx.
I did "pbc = xyz", and I downloaded the "popc.itp" from Dr. Tieleman's homepage. [ bonds ] section in "popc.itp" is okay. Running MD is okay. (It doesn't crash; no extreme velocity) It's strange that some lipids around the boundary are kept in whole molecules, but some are not. On Jan 15, 2008 12:37 PM, Alan Dodd <[EMAIL PROTECTED]> wrote: > Try using ngmx to visualise the simulation like I said, that'll tell you > exactly what bonds gromacs thinks are there and definitively confirm whether > there's a problem in the setup. > Files that may have caused the problem are of course the obvious things > like your mdp (what you've set pbc to, for instance), your topology (have > you specified the bonds correctly in the first place?). > If it turns out to just be a visualisation problem when using VMD, try > using trjconv to dump out the first frame directly as a .gro for VMD. And, > of course, using trjconv and specifying an appropriate -pbc option to 'fix' > the pbc is something to do. > ----- Original Message ---- > From: Myunggi Yi <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <[email protected]> > Sent: Tuesday, January 15, 2008 5:18:58 PM > Subject: Re: [gmx-users] image control > > 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. > > Would you let me know what simulation setup you need for the cheking? > > I used editconf to convert the .pdb file to .gro file. > Since the structure (.pdb) was pre-equilibrated one, I did setup box size > manually (not using editconf). > 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 <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 > > > ------------------------------ > Looking for last minute shopping deals? Find them fast with Yahoo! > Search.<http://us.rd.yahoo.com/evt=51734/*http://tools.search.yahoo.com/newsearch/category.php?category=shopping> > > _______________________________________________ > 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
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