[gmx-users] NVT with lipid bilayer

Justin Lemkul jalemkul at vt.edu
Sun Dec 10 03:43:56 CET 2006

Quoting Mark Abraham <mark.abraham at anu.edu.au>:

> > Hello all,
> >
> > I'm having a few more problems running an NVT ensemble on my system.  I
> > have an
> > integral membrane protein, with a transmembrane helix and small
> > extracellular
> > domain.  The bilayer is DPPC.  I have one face of the bilayer solvated to
> > surround the extracellular domain in water, and there are 3 sodium
> > counterions.
> >  I have successfully energy-minimized this system to a reasonable
> > potential
> > energy (as mentioned previously on the list).  I want to run short NVT and
> > NPT
> > equilibration steps before running full-out MD simulations.  I'm having
> > some
> > trouble getting it started.  I have attached my nvt.mdp file below, along
> > with
> > an excerpt from my md.log file that highlights the problem.  Is there
> > something
> > obvious I'm missing?  No matter what I try, the temperature and pressure
> > at Step
> > 0 are always something extremely high.
> Have you done the minimization with the constraints enabled? Whether or
> not this is true, you probably want to use unconstrained_start = yes,
> since the constraint algorithms are routinely applied after the
> integration step.

Using unconstrained_start = yes seems to have alleviated my problems.  My NVT
simulation ran nicely, and my NPT is currently going well.  Thank you very


Justin A. Lemkul
Department of Biochemistry
Virginia Tech

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