Chris, Dan
Many thanks for the useful comments
George
> On 17 Apr 2017, at 15:58, Chris Neale <candrewn.gmail.com> wrote:
>
> Be aware that if you used a variety of different starting structures and if
> the differences between starting structure is larger than the variation
> within individual trajectories, then the PCA is going to be dominated by
> the initial structures rather than the simulation dynamics. I'm not saying
> that this invalidates the approach, just something to keep in mind.
>
> On Mon, Apr 17, 2017 at 7:25 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> It is legitimate, and can be a good way to assess convergence between
>> independent trajectories. See e.g.:
>>
>> http://pubs.acs.org/doi/abs/10.1021/ct400862k
>> http://pubs.acs.org/doi/abs/10.1021/jp4125099
>>
>> Scripts for performing "combined PCA" with cpptraj are in supporting
>> information.
>>
>> -Dan
>>
>>
>> On Mon, Apr 17, 2017 at 9:19 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>> This is a general question regarding PCA.
>>>
>>> Is it legitimate to concatenate independent trajectories (same complex,
>> receptor, ligand; same topologies) and then conduct PCA on the combined
>> trajectory?
>>>
>>> Thanks in advance for any suggestions
>>>
>>> George
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>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
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>>
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Received on Mon Apr 17 2017 - 07:30:02 PDT
