[gmx-users] PCA and FEL

[sun]

Thank you very much Sir. I get you. Is it good enough to probe the stability of complex by projecting any two variables with free energy? like RMSD and Rg? 


Sent from my iPhone

> On 15-May-2016, at 10:51 am, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> 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}' >
> combined.xvg
> 
> You will loose the labels, but that should be fine.
> 
> You can combine other variables in a similar manner.
> 
> Hope it helps,
> 
> Tsjerk
> 
>> 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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