[gmx-users] how do position restraints work??

Marc Ceruso mceruso at physbio.mssm.edu
Tue Jul 29 06:54:01 CEST 2003

On Mon, 28 Jul 2003, Vivek Raut wrote:

> is fixing the atoms ( by defining a fixgroup in the .ndx file & then fixing
> that group in x, y, z directions. . eg: freezegrps = BACKBONE     freezedim
> = Y Y Y )  same as introducing the positional restraints to the molecules
> by adding ( define = -DPOSRES ) in the .mdp files???
No: the frozen coordinates of a freeze group are not updated so they are
effectively frozen. position restraints add a harmonic restraint (default
force constant 1000 kj/mol/nm-2 ) for each atom declared in a posre.itp
file. The reference positions are taken from the -r value in grompp that
defaults to the position of the restrained atoms (defined in
posre.itp) in the starting configuration. Restrained atoms are not
FIXED and their ability to move away from the reference position depends
on the strength of the spring i.e. the force constant above. Hence what
you saw in VMD.

> i tried to follow the second method, but when i see the simulation through
> VMD software, all the restrained molecules still change their position. why
> is that???.
> -------------------------------------------------------------------------------------------------------------------------------------------
> Vivek Raut
> Graduate Research Assistant
> Department of Bioengineering
> Clemson University
> Clemson, SC- 29631. USA
> Email: vraut at clemson.edu
> Phone: 864-650-1431
> --------------------------------------------------------------------------------------------------------------------------------------------
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