[gmx-users] simulation with position constraint by a harmonic potential

Liu, Liang liu4gre at gmail.com
Tue Sep 27 16:14:38 CEST 2011

> > Thanks.
> >
> > Is this position restraint same to the one "Position Restrained MD". I
> > see some tutorial shows there are always three step to perform a
> > simulation: Energy minimization, Position Restrained MD and MD
> Simulation.
> "Always" is too strong, but this is common.
> > Is it possible to fulfill the position restraint during Position
> > Restrained MD? Thanks.
> Yes, hence the name. How well they can be fulfilled depends on the
> initial and simulation conditions.

Thanks for this information.
But how to perform a harmonic potential to all the heavy atoms of RNA?
Justin said this one should be adjusted in the posre.itp file, and what I
see in the file is all 1000. Does this means k=1000 in the equation of E = k

> Mark

Liang Liu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110927/d008929b/attachment.html>

More information about the gromacs.org_gmx-users mailing list