[gmx-users] LINCS

shahid nayeem msnayeem at gmail.com
Fri Aug 17 06:28:12 CEST 2012

Right, I have a pdb where some of the residues are missing and when I
try to simulate it I get LINCS warning in between the atom of the two
ends of missing residues. So if I use a smaller time step (0.01) for
final production run and energy minimization with setting constraint =
none, making it computationally more expensive. Will these results
will be O.K.
Shahid Nayeem

On Fri, Aug 17, 2012 at 9:37 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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
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