[gmx-users] constraint pull code / gromacs 5.0.4

[Justin Lemkul]

On 6/23/15 2:10 PM, Alex wrote:
> The pulling rate, as it appears in your mdp, is actually zero. That aside,

...which is correct if one is sampling independent windows and collecting the 
forces to reconstruct the PMF.

What is atypical is the application of a constraint rather than a harmonic 
potential.  The typical "umbrella" in "umbrella sampling."

> we do not have enough info about the system. What are the nanoparticles
> made of? What forcefield is being used? Can you use trjconv to see what's
> going on?
> Please check that your system is happy prior to pulling. The huge variation
> in forces could mean weird pulling behavior (which does happen), or that
> your particles are "breathing." Set constraints to 'none' and pull code to
> see if your system behaves. The use of constraints should be deprecated in
> general, but I fear for my life suggesting it here.

It's dangerous to make broad generalizations like "constraints should be 
deprecated."  Sometimes constraints are not appropriate (materials, crystals, 
etc).  But for the vast majority of biomolecular simulations, we really don't 
care about different vibrational states of bonds involving H, so there's zero 
purpose to running our simulations 4x slower just to collect information we 
don't need :)

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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