[gmx-users] Pull code with dummy atom as reference - not working

Justin Lemkul jalemkul at vt.edu
Wed Jul 23 22:34:14 CEST 2014

On 7/23/14, 4:04 PM, Stella Nickerson wrote:
> I want to pull a carbon particle (170 atoms in a lattice) across an
> interface between Liquid A and Liquid B.  The particle starts out in Liquid
> A with the center of mass at about x = 2.5 y = 2.5 z = 2.5.  The
> liquid-liquid interface is at about z = 5.  I want to pull the particle in
> a straight line in the positive z direction.  So I put a dummy atom (no
> interaction perameters) in Liquid B at x = 2.5 y = 2.5 z = 7.5 to use as a
> reference.  I put the dummy atom in a freeze group to keep it from moving.
>   This is my pull code in my .mdp file, plus the freeze group code (DMY is
> the dummy atom, DNP is the carbon particle):
> ; Pull code
> pull            = umbrella
> pull_geometry   = distance      ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes           ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = DMY
> pull_group1     = DNP
> pull_rate1      = -0.01          ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000          ; kJ mol^-1 nm^-2
> ; Define dummy atom as freeze group
> freezegrps = DMY
> freezedim = Y Y Y
> At first I used a negative pull rate because this tutorial (
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html
> )
> says to use a negative pull rate if you want to decrease the distance
> between pull_group0 and pull_group1.  But instead of moving in a straight
> line in the positive z direction, the particle moved in the negative z
> direction at an angle (could this be because of periodic boundary
> conditions?)

The negative pull_rate doesn't make sense when the reference group has a larger 
z-coordinate than the pulled group.  Perhaps I need to clean up that language in 
the tutorial.  Here, a positive pull_rate or "direction" geometry with pull_vec1 
specified explicitly should do what you want.

> When I tried to use a positive pull rate the particle just shuffled around
> in a little x-y circle.

Try direction or position geometry with an explicit pull vector.  You may also 
need to toy with the value of pull_k1, depending upon the viscosity of your 
liquids (resisting the movement of a large particle).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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