[gmx-users] more than one peptide in one simulation box

[shahid nayeem]

Hi Mark
How one should be certain that this much  trajectory is long enough to get
coverged ensemble.
Shahid



On 4/27/10, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> On 27/04/2010 8:58 PM, Justin A. Lemkul wrote:
>
>>
>>
>> shahid nayeem wrote:
>>
>>> Dear Mark
>>> Following your advice I started using three peptide in one simulation
>>> box. Iwas able to add these with genconf as previously in ordered
>>> manner, generated .gro with genconf, solvated it and after energy
>>> minimization I did MD run for 10ns. Everything ran well. In the end
>>> when I see the trajectory I find unfolding of the original chain but
>>> the two additional peptide introduced through genconf show appearance
>>> of new secondary structures. Even in these two the secondary structure
>>> do not develop at the same point. Why the three equivalent peptide
>>> behave differently in similar environment. How can I explain this
>>> observation. why the first peptide does not show any new secondary
>>> structure. Sholud I go with higher number of molecule. Will it make
>>> any difference if peptides are added in disordered manner and then
>>> simulated.
>>>
>>
>> Initial orientation should likely have nothing to do with it. Perhaps
>> this is even the proper behavior for whatever your peptide is. Is its
>> structure dynamic? Is the size of your peptides large enough to even
>> believe that they would be intrinsically stable? Many model peptides, in
>> isolation, have very transient structures.
>>
>> It could also be that your simulation parameters are poorly chosen, so
>> the force field is breaking down. If you want comments on your .mdp
>> file, please post it.
>>
>
> Indeed. MD is chaotic, and there's no reason to expect all peptides of any
> length to show the same actual behaviour in a trajectory. They might show
> the same behaviour in the limit of a converged ensemble, but only if
> aggregation is not a factor.
>
> Mark
>
>
>  On 4/23/10, *Mark Abraham* <Mark.Abraham at anu.edu.au
>>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>>
>>> On 23/04/10 13:16, shahid nayeem wrote:
>>>
>>> Dear All
>>> I am trying to study inter peptide interaction fpr which I need
>>> to put
>>> more than one peptide in one simulation box. I did it with genconf
>>> command but this inserts peptide in a regular ordered manner I want
>>> these to be in irregular disordered insertion. Even after using
>>> genconf
>>>
>>>
>>> Well that's a difficult and atypical scenario. genconf -shuffle will
>>> allow you to stack the same peptide in a regular array with random
>>> rotations of the whole box. Then you can solvate, equilibrate and
>>> run MD at a high temperature to give yourself a quasi-disordered
>>> starting state.
>>>
>>> , I tried to proceed furthe after solvation with spc water. The
>>> energy
>>> minimization (steepest descent) failed to converge even after
>>> 5000 steps
>>> and theirafter position restraint dynamics failed giving
>>> segmentation
>>> fault. Introducing more peptide after generating .gro with -ci -nmol
>>> gives error showing more than one residue in insert molecule.
>>> Please help me and write commands which I should follow.
>>>
>>>
>>> No, because that's an impossible task. We can't begin to guess the
>>> reasons for things failing without seeing the actual output (was the
>>> EM energy large and negative? what was the actual error message
>>> from -ci -nmol?).
>>>
>>> You should be careful to start with a small test case so that you
>>> can learn the workflow with a manageable problem. Can you get a
>>> single peptide to equilibrate? Two stacked peptides? It is best to
>>> learn to walk before trying to run :-)
>>>
>>> Mark
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>>>
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