[gmx-users] LINCS

[shahid nayeem]

I want to simulate without building the missing residue. Does gromacs
have an option of capping. I am using Gromacs 4.5.4. If not then
suggest some software which I may use.
Shahid nayeem

On Fri, Aug 17, 2012 at 10:03 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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>
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