On 29/02/2012 1:11 AM, lina wrote:
On Tue, Feb 28, 2012 at 10:07 PM, Steven Neumann<[email protected]> wrote:
Thank you Vedat!
Why do you use -DFLEXIBLE in md and in em?
Why dont you use constraint algorithm (LINCS) in your simulation?
Otherwise, the system is easily explode with lots of LINCS warning.
That could well be the phenomenon referred to at the end of
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. If you
equilibrate with a small time step, you should be able to simulate with
constraints, which is more efficient and probably a better model of real
physics.
Mark
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