[gmx-users] image control

Tue Jan 15 23:12:38 CET 2008

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 <jalemkul at vt.edu> wrote:

> 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> <
> > > 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><
> 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 <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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