[gmx-users] Question about NVT

Mark Abraham Mark.Abraham at anu.edu.au
Sat Dec 2 22:05:29 CET 2006

Justin Lemkul wrote:
> Hello all,
> I have a quick question regarding an MD simulation I am attempting to run
> (again, the membrane protein which I had problems with previously).  Thanks to
> the helpful suggestions; my system is now well-minimized!  The last step before
> I would like to take before running full-out MD on my system is to equilibrate
> my solvent and ions over a short timeframe (100ps).  My initial attempts have
> been unsuccessful; the equilibration proceeds nicely for 960 steps (1.920 ps)
> before I get a screen full of LINCS warnings.  Apparently one of my DPPC
> molecules is being blown apart.  I have placed position restraints on both my
> protein and my bilayer, in order to allow the solvent and ions (Na+) to move
> around them.  I have attached my equil.mdp file below, in case I am making any
> obvious mistakes.  I am piecing my .mdp file together from several examples and
> tutorials.

Don't couple temperature for ions and solvent seperately. Make a 
combined group and couple that.

Have you tried visualising you equilibration through to the point things 
start exploding? That may highlight a problem.


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