[gmx-users] Distance restraints

David spoel at xray.bmc.uu.se
Sun Dec 19 14:16:59 CET 2004

On Sun, 2004-12-19 at 12:24 +0000, John Simms wrote:
> Hi All,
> I am using distance restraints to force a membrane protein (rhodopsin) into an "active" conformation. I have used 2 sets of distance restraints to a) maintain the secondary structure and  b) for the conformational change but nothing seems to be happeneing (after 5ns). In the .mdp file i have used 
> disre = simple
> disre weighting = conservative
> and have checked the tpr file and the conformational change restraints are present there. Furthermore, i have also run the simulation at 300C to try to overcome energy barriers. Non of this seems to work. I am being a bit naive to how these restraints work?
> Any help would be gratefully accepted
Is it  a protein conformational change, or is it a change in a ligand
(like the cis-trans isomerization in retinal in BR)?

Is the force constant large enough?

Is the distance restrains "energy" term present in your output file?

> 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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