[gmx-users] image control

Tue Jan 15 22:35:23 CET 2008

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 <tsjerkw at gmail.com> 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 < jalemkul at vt.edu> wrote:
>
> > Quoting Myunggi Yi < myunggi at gmail.com>:
> >
> > > 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 <anoddlad at yahoo.com> 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 <myunggi at gmail.com>
> > > > To: Discussion list for GROMACS users < gmx-users at 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>
> > > >
> > > >
> > > > -----Inline Attachment Follows-----
> > > >
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> > >
> > > --
> > > 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
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
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>
>
>
> --
> 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
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-- 
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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