[gmx-users] Harmonic COM Restraints with the Pull Code

Eric Dybeck ecd4bd at virginia.edu
Sun May 10 03:55:46 CEST 2015

Hello All,

I am looking to run a set of simulations in which molecules are slowly
restrained to their COM positions. To provide some context, I am going to
melt a solid, and I would like to restrain the molecules first so that they
remain in their lattice position as the melting takes places.

I believe that I can achieve this using the pull code, although I've never
used this feature in gromacs before. As I understand it, the settings in my
.mdp file should look something like:

; Pull code
pull            = umbrella
pull_geometry   = distance
pull_dim        = Y Y Y        ; 3D harmonic restraints
pull_start      = yes           ; define initial COM distance > 0
pull_ngroups    = 1          ; This may need to be the number of molecules
pull_group0     =              ; Reference molecule
pull_group1     =              ; Restrained Molecule
pull_rate1      = 0          ; No pulling rate, I am just keeping them in a
fixed position
pull_k1         = 1000     ; This number I will vary along the alchemical

In most of the pull code examples that I've seen, one atom group in the
simulation is being pulled away from another atom group also in the
simulation. In this case, the groups in the simulation will need to get
pulled toward a fixed 'reference' point that is defined based on an initial
configuration that I can supply. Is this doable? Obviously I could also
give an absolute (X,Y,Z) coordinate of the desired COM based on the initial
.gro file if that is easier to do.

Also, I will need to restrain all the molecules in the solid, rather than
just a single molecule. Is it possible to have ~100 groups harmonically
restrained with the Pull code?

Thanks for your help,

More information about the gromacs.org_gmx-users mailing list