[gmx-users] position restrained MD run?

[Samuel Flores]

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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