[gmx-users] LINCS

[Mark Abraham]

On 17/08/2012 2:56 PM, shahid nayeem wrote:
> 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.

All you can do is use pdb2gmx as you do for the normal termini. pdb2gmx 
-chainsep helps you choose where the extra termini go. pdb2gmx -h is 
your friend.

Mark

> 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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