[gmx-users] image control

[Myunggi Yi]

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.
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.


>
> -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
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