[gmx-users] image control

Tue Jan 15 20:19:53 CET 2008

Thank you.

First, I confirmed the broken lipid with ngmx.

I did "pbc = xyz", and I downloaded the "popc.itp" from Dr. Tieleman's
homepage.
[ bonds ] section in "popc.itp" is okay.
Running MD is okay. (It doesn't crash; no extreme velocity)

It's strange that some lipids around the boundary are kept in whole
molecules,
but some are not.

On Jan 15, 2008 12:37 PM, Alan Dodd <anoddlad at yahoo.com> wrote:

> Try using ngmx to visualise the simulation like I said, that'll tell you
> exactly what bonds gromacs thinks are there and definitively confirm whether
> there's a problem in the setup.
> Files that may have caused the problem are of course the obvious things
> like your mdp (what you've set pbc to, for instance), your topology (have
> you specified the bonds correctly in the first place?).
> If it turns out to just be a visualisation problem when using VMD, try
> using trjconv to dump out the first frame directly as a .gro for VMD.  And,
> of course, using trjconv and specifying an appropriate -pbc option to 'fix'
> the pbc is something to do.
> ----- 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 5:18:58 PM
> Subject: Re: [gmx-users] image control
>
> 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.
>
> Would you let me know what simulation setup you need for the cheking?
>
> I used editconf to convert the .pdb file to .gro file.
> Since the structure (.pdb) was pre-equilibrated one, I did setup box size
> manually (not using editconf).
> 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>
> >
> >
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> >
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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>
>
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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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