[gmx-users] RE:Distance restraints

David spoel at xray.bmc.uu.se
Sun Dec 19 15:05:34 CET 2004

On Sun, 2004-12-19 at 13:31 +0000, John Simms wrote:
> Hi David,
> Thanks for the quick reply, Do you ever go home :-).
I am home...
> Its a protein conformational change i have gotten the info from spin-spin couplings, zinc fingers and disulphide bridges. I have just used the default fc of 1000 in the mdp file but the multiplication factor in the 
> DISRES file is 2 for the restraints which maintain the secondary structure and 25 for the conformation change restraints. I am going this in a simulated lipid bilayer would i be better advised to do it in a vacuum?
Maybe you could check your protocol in vacuum and if you get it going
use a more realistic environment. There could be high energy barriers
between the two conformations. A free energy perturbation protocol might
be more suited.
> Cheers
> John 
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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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