[gmx-users] PCA and FEL

Tsjerk Wassenaar tsjerkw at gmail.com
Sun May 15 07:21:39 CEST 2016

Hi Suniba,

No, with gmx anaeig you can select -2d, which does a 2D projection onto the
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
to do that is something like:

paste <(grep -v '^[@#]'  proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' >

You will loose the labels, but that should be fine.

You can combine other variables in a similar manner.

Hope it helps,


On Sun, May 15, 2016 at 5:33 AM, sun <sun.iba2 at gmail.com> wrote:

> Hello everyone
> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis
> for the stability of my pro-lig complex.   In a 2015 paper, The group
> calculated two principal component, PC1 and PC2 and then prepared an.xvg
> file to be used as input for g_sham. My question is, when we use g_anaeig;
> we get eigenvec.xvg. from -comp flag. Now how shall one select two
> principal components from that data? I am sorry if my question is wrong but
> please help me.
> My second question is, can we use any two parameters like rmsd and Rg for
> input in g_sham to probe the stability of complex? Is that valid?
> With Regards
> Suniba
> Sent from my iPhone
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Tsjerk A. Wassenaar, Ph.D.

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