[gmx-users] position restrained MD run?

[Tsjerk Wassenaar]

Hi Samuel,

If you want to close your protein, you can try to set a
position_restraint between the outer ends away from the hinge.

Hope it helps,

Tsjerk

On 8/8/05, Samuel Flores <samuel.flores at yale.edu> wrote:
> Hmm... what key phrases am I looking for in the archive?
> 
> Sam
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Kai Zhuang
> Sent: Monday, August 08, 2005 12:11 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] position restrained MD run?
> 
> woah... that's an interesting idea.  I want to do the opposite, drive a
> protein
> from close to open conformation.
> 
> normal position restraint or freeze wouldn't work because you want the
> arms connected to the hinge to be able to move.
> 
> check the archive, i remember seeing a post about this a few weeks ago.
> 
> On 8/8/05, Samuel Flores <samuel.flores at yale.edu> wrote:
> > It was a PBC problem, thanks!  I set editconf flag -d 1.5 (was 1.0 before)
> > and problem went away.
> >
> > Is it possible to independently rigidify two substructures in GROMACS?  I
> > want to make two substructures of my protein rigid, and then drive them
> from
> > the open to the closed conformation, leaving the hinge flexible, as I've
> > seen in some papers.  Simply using posre.itp wouldn't work, because then
> the
> > whole protein would basically become a brick.
> >
> > Sam
> >
> > -----Original Message-----
> > From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> > On Behalf Of David
> > Sent: Monday, August 08, 2005 2:28 AM
> > To: Discussion list for GROMACS users
> > Subject: Re: [gmx-users] position restrained MD run?
> >
> > On Sun, 2005-08-07 at 22:14 -0400, Samuel Flores wrote:
> > > Howdy all,
> > >
> > > I wonder if someone can help me do a position restrained MD run.  I have
> > > read that when using a water box it is advisable to remove close
> contacts
> > in
> > > this way.  However when I do the analysis, I find protein atoms being
> > thrown
> > > unnaturally large distances.  This would not happen if the position
> > > restraints were working!  The protein should be frozen, and only the
> water
> > > would move.
> > You sure that these are not PBC effects?
> >
> > >
> > > When I go to look at the cpeptide demo script, I find that a position
> > > restrained run is being done.  However when I view the cpeptide_pr
> > > trajectory in ngmx, I see that the protein is not restrained at all, but
> > > rather is wiggling happily in the water!
> > >
> > Restrained != frozen.
> > Restraints mean that the atoms can move about the restrained positions.
> > The average position should be very close to the restrained positions.
> >
> > > What is going on?  Is it possible to do a position restrained run?  If
> > > someone could tell me why it's not happening in the cpeptide demo, I
> could
> > > make it work in my script.  I've had colleagues come look at the
> problem,
> > > banged my head against the wall, and gotten nowhere.
> > >
> > > Any help is much appreciated!
> > >
> > > Thanks
> > >
> > > Sam
> > >
> > >
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> 
> Kai Zhuang
> BioMedical Engineering @ University of Toronto
> kai dot zhuang at gmail dot com
> 6478314789
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