[gmx-users] LINCS

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 17 06:07:00 CEST 2012

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.


More information about the gromacs.org_gmx-users mailing list