[gmx-users] PCA and FEL
sun
sun.iba2 at gmail.com
Sun May 15 10:19:54 CEST 2016
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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>
>
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> Tsjerk A. Wassenaar, Ph.D.
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