Re: [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  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  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  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  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.
>>> --
>>> Gromacs Users mailing list
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> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
> Gromacs Users mailing list
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Re: [gmx-users] PCA and FEL

[Tsjerk Wassenaar]

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  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  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  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
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
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> send a mail to gmx-users-requ...@gromacs.org.
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
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Re: [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  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  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
>> --
>> Gromacs Users mailing list
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
> 
> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] PCA and FEL

[Tsjerk Wassenaar]

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  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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
Tsjerk A. Wassenaar, Ph.D.
-- 
Gromacs Users mailing list

* Please search the archive at 
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