[gmx-users] Correct method to do Cartesian PCA

[Bin Liu]

Hi Tsjerk,

I used trjconv -pbc and trjconv -nojump to remove PBC and jump across the
boundary before I applied  g_covar. This paper is about dPCA indeed. But it
also contains the author's results on cPCA. Thank you for your help.

Regards,

Bin



Message: 6
Date: Thu, 7 Jan 2016 23:38:44 +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:
        <CABzE1ShYQdeG4Sexss5QtJCy7qfg8s+2Jsh3PMChuFh4xnr7tg at mail.gmail.com>
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Hi Bin,

The procedure is correct, provided you ensured that the input trajectory
did not have PBC jumps. But the paper you refer to is on dihedral angle
PCA...

Cheers,

Tsjerk
On Jan 7, 2016 23:06, "Bin Liu" <fdusuperstring at gmail.com> wrote:

> Hi All,
>
> I am trying to reproduce the Cartesian PCA results for ALA3 in water by
> Altis et al. (Fig.2 of Dihedral angle principal component analysis of
> molecular dynamics simulations.   http://dx.doi.org/10.1063/1.2746330 )
> It is probably the most well-known PCA analysis results. I created a
system
> as they suggested and got a 100 ns trajectory (after an equilibration
> stage) for applying PCA.
>
> GROMOS96 43a1
> SPC water
> 300 K, 1 atm
> PME
> cutoff 1.0 nm
> Box larger than they did, 2100~ waters
>
> As all the PCA tutorials indicate, applying Cartesian PCA can be as simple
> as two commands, g_covar and g_anaeig. However with all my effort of
trying
> all the combinations of arguments I can think of, I still can't reproduce
> the literature results. Here I humbly request help from experienced users
> who have applied PCA before.
>
> The following is my approach. Suppose I have a .tpr file
*npt_pr_100ns.tpr*
> and a .trr file *npt_pr_100ns.trr*
>
> *g_covar -s npt_pr_100ns.tpr -f npt_pr_100ns.trr -o eigenval.xvg -v
> eigenvec.trr -av average.pdb -l covar.log*
> Choose a group for the least squares fit
> Group     0 (         System) has  6518 elements
> Group     1 (        Protein) has    22 elements
> Group     2 (      Protein-H) has    16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> Choose a group for the covariance analysis
> Group     0 (         System) has  6518 elements
> Group     1 (        Protein) has    22 elements
> Group     2 (      Protein-H) has    16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> *g_anaeig -v eigenvec.trr
> -f npt_pr_100ns.trr -s npt_pr_100ns.tpr -2d 2dproj.xvg -first 1 -last 2*
>
> Select the index group that was used for the least squares fit in g_covar
> Group     0 (         System) has  6518 elements
> Group     1 (        Protein) has    22 elements
> Group     2 (      Protein-H) has    16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> Select an index group of 22 elements that corresponds to the eigenvectors
> Group     0 (         System) has  6518 elements
> Group     1 (        Protein) has    22 elements
> Group     2 (      Protein-H) has    16 elements
> ...
> Select a group: 1
> Selected 1: 'Protein'
>
> Is there anything I did incorrectly?  Another question: is -mwa argument
> which turns on mass weighting for g_covar necessary?  Thank you very much.
>
> Best Regards,
>
> Bin
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