Hi David,
Thanks for your suggestion.
However, I have a problem with the use of distance restraints in gromacs. As
described in the manual a restraint potential is applied to each pair of atoms
separately. Instead, I would like the restraint potential to depend on the
root mean square of pair distance deviations, i.e. distance-based RMSD as you
suggest.
Maybe I can use the "averaging over multiple pairs" facility, If I change the
averaging function (power 2 instead of 6) ?
Thanks again,
Sam
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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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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