Another possibility is to patch gromacs with PLUMED
http://merlino.mi.infn.it/~plumed/PLUMED/Home.html
Here RMSD (and derivatives) is already implemented and you can
easily restraint your MD simulation within a certain RMSD cutoff
from a reference structure.
Massimiliano
On May 19, 2009, at 9:31 AM, David van der Spoel wrote:
Sam Moors wrote:
Hi,
Position restraints do not allow me to do what I want.
For instance, I want to allow the system to freely explore the
conformational space within a certain RMSD range, but not evolve
beyond a specified RMSD cutoff.
Another application would be to push the system conformation away
from the reference structure, by using negative force constants.
Therefore the reference structure should be fitted to the
simulation structure (or the other way around) before calculating
the position differences.
Then you have to derive a force that is the derivative of the RMSD
with respect to the positions. This may be difficult, since you have
the superposition step in between. What you could do straight away
is move from normal RMSD to distance-based RMSD, in which case the
this has been implemented using distance restraints. You would use
genrestr to generate the additional topology input, then determine a
suitable force constant and Bob's your uncle.
Cheers.
Thanks in advance for your help,
Sam
Mark Abraham wrote:
Sam Moors wrote:
Hi gmx users/developers,
I would like to do a molecular dynamics simulation with a
restraint on
the backbone RMS deviation from a reference structure.
Does anybody know if this is possible?
How about position restraints only on the backbone? Same effect.
Not exactly as you describe, but you should read the section in
chapter
4 of the manual and see for yourself.
If yes, could you explain how to do it?
If no, what would be the easiest way to implement this in gromacs?
It could be done, but I'm not sure it's worth the effort.
Mark
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University.
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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