[gmx-users] Constraints & Restraints

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 13 00:05:45 CET 2009

Darrell Koskinen wrote:
> Thanks for the additional comments.
> So given that, in my system, I have H atoms attached to C atoms on the 
> perimeter of a finite graphene sheet that is placed above multiple 
> infinite layers of graphene (graphite), would it be more appropriate to 
> use: (i) a classical (harmonic) model using constraints=none or (ii) a 
> constrained model using constraints=all-bonds?

Is there a precedent established in the literature?  Spectroscopic data that can 
justify your choice?  Constraints are generally reasonable for bonds that are in 
the ground state, so your choice will also be motivated by the conditions you're 
trying to simulate.

> Note that, currently, I use constraints=none and see that the C atoms in 
> the graphene sheet are well behaved and not vibrating very much, but the 
> H atoms on the perimeter are vibrating wildly. Would you have any idea 
> of whether this is natural and to be expected or not? Maybe this is an 
> indication that constraints should be used in this particular model. 
> However, I have no idea whether it is natural for hydrogen atoms to flip 
> and flop around so much on the edge of a graphene sheet.

I guess it depends on what you mean by "wildly."  It could just be that you're 
using too large of a time step, generating an unstable trajectory.  In the 
absence of constraints, you cannot necessarily guarantee stable integration with 
dt greater than 1 fs.  Again, spectroscopic information (if available) would 
probably give you an indication on the vibrational frequencies of bonds 
involving hydrogen atoms.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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