[gmx-users] LINCS

[Mark Abraham]

On 17/08/2012 2:28 PM, shahid nayeem wrote:
> 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.

Does it sound OK to model missing residues with solvent (or vacuum) and 
have a chemical bond between the dangling ends? It's also definitely not 
OK to ignore the warning pdb2gmx gave you about this bond being too 
long. Plowing ahead blindly costs more time than than being careful and 
painstaking.

You need to either cap your chains or build in the missing residues with 
non-GROMACS software, but what's best depends what you're trying to observe.

Mark

> 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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