[gmx-users] Correct method to do Cartesian PCA

[Antonio Baptista]

On Fri, 8 Jan 2016, Bin Liu wrote:

> Hi Tsjerk,
>
> I replicated their settings in their papers. The system size I used is
> larger than what they had. Could you elaborate on the reference used for
> fitting? Thank you so much.

About the importance of the reference structure used for fitting in 
Cartesian PCA, you may want to look at this: 
http://dx.doi.org/10.1021/jp902991u

Best,

--
Antonio M. Baptista
Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa
Av. da Republica - EAN, 2780-157 Oeiras, Portugal
phone: +351-214469619         email: baptista at itqb.unl.pt
fax:   +351-214411277         WWW:   http://www.itqb.unl.pt/~baptista
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>
> Cheers,
>
> Bin
>
> Message: 3
> Date: Fri, 8 Jan 2016 18:29:26 +0100
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Correct method to do Cartesian PCA
> Message-ID:
>        <CABzE1Sg7rSq5eZod0wBrPLcVWMG32S__xG0D2+aFzKj6YRpYiQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi Bin,
>
> Did you use the same force field, simulation length, other parameters? The
> system size might play a role too. And for trialanine the reference used
> for fitting may matter too. But first check all the other
> similarities/differences.
>
> Cheers,
>
> Tsjerk
> -- 
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