[gmx-users] DPPC bilayer simulation crash

Pedro Alexandre de Araújo Gomes Lapido Loureiro palaplou at gmail.com
Fri Apr 6 14:47:10 CEST 2007

Hi Michael,

are you simulating with a constant area, volume or pressure ensemble?
If you are using the configuration you mention as a starting point and
simulating it with another forcefield, as Mark pointed out, it's not
unexpected to find problems.
Moreover, equilibration in lipid simulations... takes time!! At least 10-20
ns of simulation, as a rough estimate.
If you are using constant area or volume, observe that a DPPC bilayer has
an experimental area per lipid of 64 A**2 at 50 C, so you should start with
this value.
Regarding constant pressure simulations, your system must reach that value.



2007/4/6, Mark Abraham <Mark.Abraham at anu.edu.au>:
> Michael Skaug wrote:
> > I am trying to perform a simulation of 128 dppc in 3655 spc water.
> > I obtained .pdb and .top files from the Biocomputing website at
> U.Calgary.
> >  I do nothing to alter the structure, which must be minimized as it
> comes
> err, not minimized - sampled from the ensemble they were using, which
> needn't correspond to the ensemble you're using. As soon as you generate
> new velocities, the source of your structure will only give you the same
> gross morphology, not an equilibrated system.
> > from the end of a 1 ns simulation.  Processing the input files works
> fine,
> > but the mdrun always ends somewhere between step 500 and step 3000.  I
> have
> > tried adjusting various parameters, such at the time step, tau_p, tau_t
> and
> > the compressibility, but nothing has created a consistent run.
> > I wonder where I should be focusing my time to solve this
> problem.  Should
> > I focus on the parameters and structure, or computer hardware/software?
> We can't tell unless you tell us what GROMACS is reporting as the problem.
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