[gmx-users] Keeping PBC during minimization

[Justin A. Lemkul]

Francesco Rao wrote:
> Dear all
> 
> I have a water box (without any protein or ion). I would like to
> minimize the box using PBC. My input file looks something like:
> 
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> pbc = xyz
> emtol           = 0.1           ; Stop minimization when the maximum
> force < 1.0 kJ/mol
> nsteps          = 2000         ; Maximum number of (minimization)
> steps to perform
> nstenergy       = 10            ; Write energies to disk every nstenergy steps
> ns_type         = grid
> 
> The problem is that just before the Steepest descent is called PBC are
> removed (!)
> 
> Enabling SPC water optimization for 216 molecules.
> Removing pbc first time
> Done rmpbc
> Initiating Steepest Descents
> 
> HOW DO I FORCE PBC TO STAY??
> 

There's no need to shout :)

"Removing pbc" does not mean you lose periodic boundary conditions, I believe it 
means that molecules "broken" across periodic boundaries are made whole at the 
first step.

-Justin

> thanks
> 
> F
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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