[gmx-users] The loops run far away

[Tanping Li]

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?


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
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the 
> www interface or send it to
> gmx-users-request at gromacs.org.
>