[gmx-users] PCA and FEL

[sun]

Allright Sir
Thank you very much for clearing the point. 
With Regards
Suniba

Sent from my iPhone

> On 15-May-2016, at 12:14 pm, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> Hi Suniba,
> 
> No, you will get the stability of configuration in the order parameters you
> choose. But you don't know how much conformational freedom you have at each
> point. Low RMSD will mean stable, but a fixed point at high RMSD does not.
> Also note that the Rg is sort of part of the RMSD, which can be written as
> Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters
> will be correlated.
> 
> Cheers,
> 
> Tsjerk
> 
>> On Sun, May 15, 2016 at 8:13 AM, sun <sun.iba2 at gmail.com> wrote:
>> 
>> 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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>>> 
>>> 
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
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