Thanks a lot for all the advice from Paul, carols and Samuel. It seems the maximum correlation time is very important for the calculation.
Now I tried to calculate the order parameter using IRED approach and had the exact same problem as Samuel.
http://archive.ambermd.org/200806/0316.html
I got the same autocorrelation function for all the NH vectors. Samuel, can you help out?
Here is my input file: (only use three residue for simplicity)
trajin test.mdcrd
vector r2 :2.N corr :2.H
vector r3 :3.N corr :3.H
vector r9 :9.N corr :9.H
matrix ired order 2 name nhma
analyze matrix nhma out nhmr vecs 7
vector r2 :2.N corrired :2.H modes nhmr begin 1 end 3 npair 1
analyze timecorr vec1 r2 vec2 r2 out r2.nh tcorr 500. tstep 2.0 norm out r2.nh
vector r3 :3.N corrired :3.H modes nhmr begin 1 end 3 npair 2
analyze timecorr vec1 r3 vec2 r3 out r3.nh tcorr 500. tstep 2.0 norm out r3.nh
vector r9 :9.N corrired :9.H modes nhmr begin 1 end 3 npair 3
analyze timecorr vec1 r9 vec2 r9 out r9.nh tcorr 500. tstep 2.0 norm out r9.nh
all the best
thQuoting Samuel Genheden <samuel.genheden.gmail.com>:
> Hi
>
> We've started to abandon the autocorrelation approach, just because
> the problems with convergence. You have to look carefully on each
> residue to see if they have really converged or not. Therefore, we
> recommend to use iRED instead. On our test cases we haven't observed
> any large overall difference between iRED and
> autocorrelation-approach, but the latter requires more hands-on job.
>
> / Samuel
>
> 2010/5/1 Paul S. Nerenberg <psn.berkeley.edu>:
>> Hi,
>>
>> Your e-mail is unclear in terms of what you mean by "negative value of the
>> auto-correlation function". It is not unexpected that the auto-correlation
>> function becomes negative at some correlation time (tau), although it should
>> usually be fluctuating around zero when this happens (i.e., not reaching a
>> large negative value). Moreover, if you were to average your C(tau)
>> calculation over several trajectories, then you should see that these
>> fluctuations about zero generally become smaller (as this "noise" is
>> averaged out).
>>
>> So long as your simulations are adequate in length with regards to the max.
>> correlation time and you are reasonably certain that your system can be
>> analyzed with the model-free approach (which is nothing more than a *model*
>> that makes assumptions about the dynamics of your molecule), then you should
>> not have a problem fitting your auto-correlation functions to that
>> exponential form.
>>
>> Best,
>>
>> Paul
>>
>> P.S. The max. correlation time used in your analysis (and correspondingly
>> your simulation length) should always be chosen with regard to the
>> characteristic relaxation times of your molecule, as is explicitly
>> demonstrated in the article that Carlos referenced. I'm sure that the more
>> NMR-minded AMBER users out there probably have some other pointers as
>> well...
>>
>>
>> On Apr 30, 2010, at 2:39 PM, luzhenw1.msu.edu wrote:
>>
>>> Thanks for the information. I read the Bruschweiler paper for the IRED
>>> method and think it is OK to not use IRED approach. The question still
>>> remains.
>>>
>>> Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
>>>
>>>> this is a useful article for such calculations
>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426661/
>>>>
>>>>
>>>> On Fri, Apr 30, 2010 at 4:43 PM, <luzhenw1.msu.edu> wrote:
>>>>
>>>>> According to model-free formalism, the internal correlation function of
>>>>> NH
>>>>> vector, CI(t)=S^2+(1-S^2)e^(-t/tau)>=0. I tried to calculate the order
>>>>> parameter from MD calculation. However, I got negative value of the
>>>>> auto-correlation function for some residues. Is the defination of
>>>>> autocorrelation different between NMR and MD? Thanks.
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Received on Mon May 03 2010 - 12:30:09 PDT
