[gmx-users] LINCS

[Mark Abraham]

On 17/08/2012 2:02 PM, shahid nayeem wrote:
> Dear all
>> One basic clarification. How does LINCS algorithm influences the results
>> of final production run. In what respect a minimization, pr and final
>> simulation done with constraints = none and with constraint= all_bonds are
>> different.

Sounds like you should do some background reading on how and why 
constraints work. Manual and refs therein are good starting points. Or 
your favourite molecular simulation textbook. In a nutshell, you use 
them in production simulation because they're a reasonable model and 
allow a larger time step. You might avoid them when you're not yet at 
equilbrium, because their implementation can be brittle when your 
structure doesn't agree with the model physics.

Mark