[gmx-users] The loops run far away

[David]

On Mon, 2005-08-08 at 11:37 -0700, Tanping Li wrote:
> Dear David,
> 
> The annoy thing is that the loop doesn't converge to
> the same position with the slightly different initial
> condition. I can't decide which one is correct. Does
> this mean I need to do the restrain or EM again?

Unless you have additional (experimental) information all you can do is
simulate longer and hope that they do converge. In the CVS code you
could also try REMD for increased sampling.

> 
> 
> Best
> Tanping
> 
> 
> --- David <spoel at xray.bmc.uu.se> wrote:
> 
> > On Sun, 2005-08-07 at 20:58 -0700, Tanping Li wrote:
> > > Dear all,
> > > 
> > > I am analyzing the interaction between a specific
> > > residue and close residues. The residue is very
> > close
> > > to a loop (not the N and C terminal). I solvated
> > the
> > > protein several times, loops have different
> > positions.
> > > Sometimes, it goes far away from the crystal
> > > structures. I tried my best to keep it around the
> > > crystal position, but I can't. I have struggled
> > for
> > > two weeks. Any suggestions? I looked through the
> > > mailing list, but can't find the related
> > information.
> > > 
> > You can force it using restraints, but the best
> > method is probably to do
> > a number of simulations with slightly different
> > starting conditions and
> > see whether they converge to the same results.
> > 
> > Loops are often mobile of course.
> > 
> > -- 
> > 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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-- 
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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