[gmx-users] image control

Tue Jan 15 22:58:18 CET 2008

Quoting Myunggi Yi <myunggi at gmail.com>:

> On Jan 15, 2008 2:48 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.
> >
>
> 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 <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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> >
>
>
>
> --
> 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
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================