Thank you all of you. I've got a pre-equilibrated hydrated POPC bilayer from a web-site. I made a hole, and I placed my protein. Now, what is the next step?
On Jan 15, 2008 4:58 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting Myunggi Yi <[EMAIL PROTECTED]>: > > > On Jan 15, 2008 2:48 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. > > > > > > > As I said I have already confirmed with ngmx, and I can check > > the .gro file (text file). > > > > > > > > > > > > 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. > > > > > > > I did the initial setup from pre-equilibrated pdb file. > > Then the above (.gro) is the MD result. > > > > > > > > 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. > > > > > > > Since I have pre-equilibrated system, I don't want to waste time. > > As you know If I make a large box, during the equilibration the system > will > > be distorted a lot. > > Perhaps I'm missing the purpose of what you're trying to do. Do I > understand > correctly that you have a pre-equilibrated system (.pdb) and you want to > run MD > on a similar system that is just larger? To me, that sounds like a job > for > genconf with the original .pdb file (create replicas of your system with > an > appropriate box size, not one that gets put in manually). > > If I'm misunderstanding, it might be beneficial to describe your system in > a bit > more detail so we can all understand what's going on. > > > To get the right system I need long long time equilibration. > > > > However, my question is this. > > Does this cause the image problem? > > Even though I prepare the large BOX with "editconf", I see the same > problem > > See above, regarding genconf, if that's what you're trying to do. > > -Justin > > > > > > > > > > > -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 <gmx-users@gromacs.org> > > > > > 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> < > > > http://www.scs.fsu.edu/%7Emyunggi> > > > > > > > > > > > > > > > -----Inline Attachment Follows----- > > > > > > > > > > _______________________________________________ > > > > > gmx-users mailing list gmx-users@gromacs.org > > > > > 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 gmx-users@gromacs.org > > > > > 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>< > 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 gmx-users@gromacs.org > > > 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 gmx-users@gromacs.org > 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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