A free energy calculation is converged when a longer simulation does
not change the value. One way to show this is to use cumulative
average of different trajectory lengths, i.e. 0.5s, 1ns, 1.5ns, 2ns,
2.5ns and so on to show that the value no longer changes over time.
That being said, use of complete different MD trajectories is often
more useful due to the limited sampling ability of standard MD.
Suppose you have collected a set of independent production
trajectories. You can see whether the free energy value changes if you
use one, two, three, four, five, ..., trajectories. Eventually, the
value would not show systematic change any more when more trajectories
are added to the averaging process.
Another point is that delta G for a reaction converges fast if you use
the single trajectory approach, apparently due to noise cancellation.
All the best,
Ray
On Mon, Jun 11, 2012 at 11:56 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
> Thanks for reply
>
> But what is here mean by converged?
> Is it if I am running two different MD run with same parameter then rmsd of
> these two should converged then only that trajectory used for MMPBSA
> calculation?
>
> Here I am using three trajectory method. So is here criteria of converged
> trajectory also used for ligand as well as receptor along with complex
> trajectory?
>
> Here I am attaching a rmsd graph of wt complex can I call it converged trajectory?
>
>
>
>> This just means that you have not run long enough MD trajectories,
>> i.e. your free energy calculations have not converged ... if you do,
>> the difference between different trajectories should be within the
>> uncertainties of reported free energies.
>>
>> Ray
>>
>> On Mon, Jun 11, 2012 at 2:08 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>>>
>>> Hello All
>>> I have four protein-DNA complexes first is wt, second DNA mutant, third
>>> protein
>>> mutant and fourth both mutant. I have to calculate binding free energy of
>>> these
>>> complexes.
>>>
>>> When I ran MD simulation of all these and calculate binding free energy, I got
>>> binding free energy as follows:
>>> First MD
>>>
>>> wt = -77.4 kcal/mol
>>> DNA mutant = -59.7 kcal/mol
>>> protein mutant = -77.2 kcal/mol
>>> both mutant = -73.9 kcal/mol
>>>
>>>
>>> Second MD run
>>>
>>> wt = -72.9 kcal/mol
>>> DNA mutant = -91 kcal/mol
>>> protein mutant = -74 kcal/mol
>>> both mutant = -86.8 kcal/mol
>>>
>>> Is it possible to reproduce the result? I also claulated residue wise energy
>>> decomposition there also I am getting diffrent result residue which is not
>>> involve in interaction energy of that residue in first MD run is unfavorable
>>> (2.9 kcal/mol) but in second MD run become favorable (-10.7 kcal/mol). So I am
>>> not able to justify my result.
>>>
>>> Is here my approach to claulate bindng free energy is correct, i.e. run two MD
>>> simulation and then calculation of binding free energy is correct so that I
>>> can
>>> also calculate STD of two result or run MMPBSA two times of a single MD run
>>> and
>>> calculate STD of two MMPBSA calculation ?
>>>
>>> Can anybody please suggest me
>>>
>>>
>>>
>>> With regards
>>>
>>> Sangita Kachhap
>>> SRF
>>> BIC,IMTECH
>>> CHANDIGARH
>>>
>>> ______________________________________________________________________
>>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
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>
>
> With regards
>
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jun 11 2012 - 12:30:03 PDT
