On Wed, Aug 5, 2015 at 11:39 AM, George Tzotzos <gtzotzos.me.com> wrote:
> crdaction crd1 projection T1 modes evecs.dat beg 1 end 20 :1-125&!.H= \
> crdframes 1, 2000 out T1.dat
Remove the space in your crdframes argument, e.g. 'crdframes 1,2000'.
This is the source of your error messages.
> Warning: No actions/output trajectories specified.
This is because you only have analyses set up at the end (kde etc).
Can be safely ignored.
> Warning: Size of Mode1 (10000) != size of Mode1 (8000)
> Warning: Only using 8000 data points.
This is related to your malformed crdframes arguments above - each
projection start argument was read but not the end because of the
space. So the first projection T1 had 10000 frames, the second 8000,
and so on. This will be resolved after you fix the crdframes
arguments.
Hope this helps,
-Dan
>
>
>
>
>> On 5 Aug 2015, at 20:16, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> Hi,
>>
>> This is by no means the only way, but we've done this kind of analysis
>> recently (see http://pubs.acs.org/doi/abs/10.1021/jp4125099). The idea
>> is to calculate principal components from a combined trajectory (e.g.
>> trajectories T1 + T2 + T3), then calculate projections along those
>> principal components separately (i.e. the projections for T1, T2, and
>> T3 along the combined PCs). The distributions for the individual
>> projections for PCs (particularly the low frequency ones) should
>> overlap pretty well, otherwise the trajectories are not converged -
>> note that overlap is a necessary but not sufficient condition of
>> convergence, ideally you will look at several different properties to
>> ascertain overall convergence. We used Kullback-Leibler divergence to
>> quantify the overlap of distributions, but that isn't the only way.
>> The SI in the given publication has some example scripts for CPPTRAJ
>> you should be able to adapt for your use.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Wed, Aug 5, 2015 at 2:24 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>> I’ve run 5 independent MD simulations of the same system. I’m seeking advice on how to compare the Principal Components derived from each trajectory to assess convergence of sampling.
>>>
>>> Thank in advance for any guidance and advice
>>>
>>> Regards
>>>
>>> George
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Aug 05 2015 - 11:30:02 PDT
