[gmx-users] Re: Problem running free energy simulations

Jernej Zidar jernej.zidar at gmail.com
Thu Oct 3 10:32:43 CEST 2013

Dear Michael.
  The simulations at each lambda point starts from the same structure
that I equilibrated (NPT ensemble) for 20 nanoseconds. The system has
~7500 atoms in a box the size 5 nm x 5 nm x 5 nm.  The molecule of
interest is located in the center of the unit cell.

> Sounds like the simulation is blowing up.  How soon does it start crashing.
> Also, what configurations are you using to start your free energy
> simulations at each lambda?

Windows: Re-Boot, Linux: Be-Root.

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