[gmx-users] NVT with lipid bilayer

Mark Abraham mark.abraham at anu.edu.au
Sat Dec 9 02:48:41 CET 2006

> 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
> 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.

For equilibration with RF, I tend to use tau_t as low as 0.01, but I do
not think this is your problem.


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