[gmx-users] The loops run far away

David spoel at xray.bmc.uu.se
Mon Aug 8 08:30:13 CEST 2005

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 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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