[gmx-users] Distance restraints

[David]

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 
> 
> _______________________________________________
> 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.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++