[gmx-users] position restrained MD run?

[Samuel Flores]

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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