[gmx-users] Long range forces, periodic boundaries and aggregation

Alan Dodd anoddlad at yahoo.com
Tue Sep 27 16:02:25 CEST 2005

Position restraints can be given differently for each
of the 3 axes.  Check position restraints, genpr etc.
in the manual.
The output of pdb2gmx will let you know if there's any
net charge on the molecule.  In addition, most other
programs, eg grompp, will often issue a warning if the
charge of the whole system is not zero.
I'm not sure what long-range force you're looking at,
but I'd imagine motion in a fluid will appear very
random, especially when the particles start with
neighbours equally spaced in each axis.  You'd
probably need a big force, or a long simulation
period, to see a definite effect?

--- Steven Kirk <Steven.Kirk at htu.se> wrote:

> Hello,
> Firstly, many thanks to David and the others who
> answer users questions on this list. Your help has
> been invaluable to me in the past.
> I have a large, approximately spherical
> macromolecule (silica nanoparticle, approx. 4 nm in
> diameter) which I am investigating in TIP4P water. I
> put the molecule centered in a cubic box of side 6
> nm, then build another cell which is effectively two
> of these boxes side by side in the X-direction. The
> resulting simulation cell is then 12x6x6 nm, and I
> then add TIP4P water using genbox. I am using PME
> electrostatics, with a FFT grid spacing of 0.12 nm,
> a pme_order of 6, a time step of 0.001 ps and a
> simulation run time of 80 ps. 
> My original thought was that the two nanoparticles
> (labelled 'left' and 'right' in the following, due
> to the x-axis alignment of the cuboidal cell) would
> drift slowly towards each other along the x-axis due
> to long-range forces. Instead, what seems to happen
> in the simulation is that the 'left particle' drifts
> *downward*, while the  'right particle' drifts
> *upward*. Neither particle comes very close to the
> upper or lower side of the simulation box, but the
> drift is visible in the output trajectory. g_dist
> tells me that, on average, the centers of mass of
> the particles get further apart. So far as I can
> tell, there is no net charge on each particle (how
> could I check this easily?).
> The only reason for this I can come up with is
> simply a built-in asymmetry due to the non-perfect
> spherical shape of the particles, such that the
> nearest copy of each particle lies in the
> y-direction, corresponding to the direction of
> drift.
> Could I force the relative motion of the 2 particles
> in the unit cell to be *only* along the x-axis by
> constraining the motion of their respective centers
> of mass, and would this introduce any unanticipated
> artifacts in the calculation ? Is there anything
> else I can do to make this 'slow aggregation'
> calculation faster ?
> Many thanks in advance,
> Steve Kirk
> Dr. Steven R. Kirk          <Steven.Kirk at htu.se,
> S.R.Kirk at physics.org>
> Dept. of Computer Science, TMD              
> http://taconet.webhop.org
> Univ. of Trollhattan/Uddevalla   Ph: +46 520 475318
> Fax:+46 520 475399
> P.O. Box 957 Trollhattan 461 29 SWEDEN
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