Re: [AMBER] compare two trajectories

From: Xing <stecue.gmail.com>
Date: Thu, 15 Oct 2015 22:29:08 -0400

Dear Hai,

Great! Thanks very much!

On 07/10/2015 03:41 PM, Hai Nguyen wrote:
> you can do clustering for both simulations and compare population for each
> cluster. Search Amber 15 manual for cpptraj clustering.
>
> Look at Figure 4 in this for example:
> http://pubs.acs.org/doi/full/10.1021/ct600263e
>
> Hai
>
> On Fri, Jul 10, 2015 at 3:35 PM, Xing <stecue.gmail.com> wrote:
>
>> Dear All,
>>
>> I have obtained two equilibrium trajectories of a protein using two
>> slightly different approaches. Is there a rigorous way to show that the
>> structures of the two trajectories are statistically the
>> same (and therefore the two results of the approaches are identical)? RMSD
>> with respect to their overall averaged structure and individual averages? I
>> think the energy cannot be compare because the
>> number of water molecules are different when solvating in xleap.
>>
>> --
>> Best wishes,
>>
>> Xing
>>
>>
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-- 
Best,
Xing
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Received on Thu Oct 15 2015 - 19:30:04 PDT
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