Re: [gmx-users] PCA problems

[ingram]

Still no luck

When I tried

gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -pbc nojump  I get a 
very strange trajectory and covar does not work with this


I have also tried

gmx trjconv -f md_golp_vacuo.trr -o trajectory.gro -fix transxy -pbc 
mol -s topol.tpr to generate a continuous trajectory


followed by
gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc

And still the problem remains

I also tried with -s topol.tpr and the same problem remains.


I get a similar problem with a free peptide with no periodic boundary 
conditions. It is not broken up but residues change size throughout the 
trajectory and vmd draws bonds in very odd places





So I believe I have tried to remove the effects of pbc and with a 
single reference file ffor fitting and still no luck. Can anybody 
explain to me (very simply and how gromacs implements) covar and anaeig? 
Potential problems and what I might try next.



Thanks for your time Grommunity

Teresa


On 2016-06-08 21:07, Antonio Baptista wrote:

On Wed, 8 Jun 2016, Tsjerk Wassenaar wrote:


Hey :)




 That usually gives a fitted ensemble that more closely retains the
original RMSD values between all pairs of structures.



This should read: ... a fitted ensemble of which the sum of the 
traces of

all pairwise inner product matrices is closer to minimal.
The pairwise RMSDs (and their sum) remain what they are.


Yep, I didn't phrase it the best way. Thanks for clarifying... :)



Cheers,

Tsjerk

-- Tsjerk A. Wassenaar, Ph.D.
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Re: [gmx-users] PCA problems

[Antonio Baptista]

On Wed, 8 Jun 2016, Tsjerk Wassenaar wrote:


Hey :)




 That usually gives a fitted ensemble that more closely retains the
original RMSD values between all pairs of structures.



This should read: ... a fitted ensemble of which the sum of the traces of
all pairwise inner product matrices is closer to minimal.
The pairwise RMSDs (and their sum) remain what they are.


Yep, I didn't phrase it the best way. Thanks for clarifying... :)



Cheers,

Tsjerk

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

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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hey :)



>  That usually gives a fitted ensemble that more closely retains the
> original RMSD values between all pairs of structures.
>

This should read: ... a fitted ensemble of which the sum of the traces of
all pairwise inner product matrices is closer to minimal.
The pairwise RMSDs (and their sum) remain what they are.

Cheers,

Tsjerk

-- 
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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Re: [gmx-users] PCA problems

[Antonio Baptista]

Hi James,

If your molecule shows some flexiblility, I would suggest using as a 
reference the structure of your original ensemble that produces the fitted 
ensemble with the lowest sum of RMSD values to that structure (or their 
square). That usually gives a fitted ensemble that more closely retains 
the original RMSD values between all pairs of structures.


If your molecule is well-structured, it wouldn't make much difference 
which reference you use, as Tsjerk said.


Best,
Antonio


On Wed, 8 Jun 2016, jkrie...@mrc-lmb.cam.ac.uk wrote:


ok thanks Tsjerk. I think that makes sense now.

Best wishes
James


Hi James,

That's silly! Ambiguous means that the same structure can have multiple
solutions in a fit. The fit to a single reference structure (with more
than
three atoms) is never ambiguous. Can never, by definition!

Now if you have two reference structures at hand, and they have (quite)
different structures, then fitting on one may give a different ensemble
from fitting on the other. The fit is not consistent, and the
inconsistency
is worse for flexible molecules. Different ensembles will mean different
correlations, thus giving different principal components.

Progressive fitting does not solve the problem. In fact, progressive
fitting _is_ ambiguous. Let's say we have a series of conformations ABCAC.
Then we  fit C once to B, which was fitted to A, and later we have C
fitted
to A, which was fitted to the previous C. Note that in practice the
situation will be much worse as we can approach a certain configuration
from many sides. Using B as reference will yield a fit that is different
from using A as reference, so the structure C will have two different
orientations in the resulting ensemble. Hence, the fit is ambiguous.

For structured proteins, the difference will not matter much. However, in
long trajectories there may be an added contribution (drift) of the
orientation.

Hope it helps,

Tsjerk

On Wed, Jun 8, 2016 at 5:33 PM,  wrote:


Thanks Tsjerk,

Isn't the progressive fit supposed to rotate everything back into the
same
orientation without having to worry about inferring that orientation
from
a reference structure that doesn't align well? Each configuration should
in theory align well to its predecessor all the way back to the starting
structure (which is what I'd usually take as a reference anyway).

The original note I was thinking of says as follows:

'''Before a PCA, all structures should be superimposed onto a common
reference
structure. This can be problematic for very flexible systems such as
peptides,
where the fit may be ambiguous, leading to artificial structural
transitions. In
certain cases, such problems may be alleviated by using a progressive
fit,
where
each structure is superimposed onto the previous one. It is also
important
to note
that when results of different PCAs are to be compared with each other,
then
each individual PCA should be based on the same reference structure used
for
superposition.'''

Please could you explain further what it is I have misunderstood.

Also would you say a progressive fit is a bad idea for more structured
proteins?

Many thanks
James


Hi James,

'Spurious alignment' is the dependence of the resulting ensemble on

the

reference structure. Unfortunately, that's not solved by a progressive
fit.
Rather, in a progressive fit, the same configuration can have multiple
orientations, based on the previous structures, which is also

problematic

when you're trying to understand spatial correlations between atoms

within

their reference frame.

Cheers,

Tsjerk

On Wed, Jun 8, 2016 at 9:27 AM,  wrote:


Dear Teresa,

That sounds like a periodic boundary issue to me. It could be fixed

by

using a tpr instead of a gro as the gmx covar manual says "All
structures
are fitted to the structure in the structure file. When this is not a
run
input file periodicity will not be taken into account." Alternatively

if

you don't have a tpr you could use gmx trjconv first with -pbc whole

or

-pbc nojump.

I also remember reading (I think it was in the Hayward and de Groot
review
2008) that fitting peptides to a reference structure can cause

spurious

alignments. I don't know if this is also related to what you're

seeing

but
it might be worth using gmx trjconv again with-fit progressive then

use

-nofit in gmx covar.

Best wishes
James


Dear GROMACS community

I am trying to complete a PCA analysis of my peptide adsorbed to a
surface. However when I use :

gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc

and select the protein for both the least squares fit and

covariance

calculation, followed by


gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
-first 1 -last 1 -skip 100

and I select the peptide for the least squares and covariance
calculation

My peptide is now broken up into pieces. Is this right?



Best
Teresa
--
Gromacs Users mailing list

* Please search the archive 

Re: [gmx-users] PCA problems

[jkrieger]

ok thanks Tsjerk. I think that makes sense now.

Best wishes
James

> Hi James,
>
> That's silly! Ambiguous means that the same structure can have multiple
> solutions in a fit. The fit to a single reference structure (with more
> than
> three atoms) is never ambiguous. Can never, by definition!
>
> Now if you have two reference structures at hand, and they have (quite)
> different structures, then fitting on one may give a different ensemble
> from fitting on the other. The fit is not consistent, and the
> inconsistency
> is worse for flexible molecules. Different ensembles will mean different
> correlations, thus giving different principal components.
>
> Progressive fitting does not solve the problem. In fact, progressive
> fitting _is_ ambiguous. Let's say we have a series of conformations ABCAC.
> Then we  fit C once to B, which was fitted to A, and later we have C
> fitted
> to A, which was fitted to the previous C. Note that in practice the
> situation will be much worse as we can approach a certain configuration
> from many sides. Using B as reference will yield a fit that is different
> from using A as reference, so the structure C will have two different
> orientations in the resulting ensemble. Hence, the fit is ambiguous.
>
> For structured proteins, the difference will not matter much. However, in
> long trajectories there may be an added contribution (drift) of the
> orientation.
>
> Hope it helps,
>
> Tsjerk
>
> On Wed, Jun 8, 2016 at 5:33 PM,  wrote:
>
>> Thanks Tsjerk,
>>
>> Isn't the progressive fit supposed to rotate everything back into the
>> same
>> orientation without having to worry about inferring that orientation
>> from
>> a reference structure that doesn't align well? Each configuration should
>> in theory align well to its predecessor all the way back to the starting
>> structure (which is what I'd usually take as a reference anyway).
>>
>> The original note I was thinking of says as follows:
>>
>> '''Before a PCA, all structures should be superimposed onto a common
>> reference
>> structure. This can be problematic for very flexible systems such as
>> peptides,
>> where the fit may be ambiguous, leading to artificial structural
>> transitions. In
>> certain cases, such problems may be alleviated by using a progressive
>> fit,
>> where
>> each structure is superimposed onto the previous one. It is also
>> important
>> to note
>> that when results of different PCAs are to be compared with each other,
>> then
>> each individual PCA should be based on the same reference structure used
>> for
>> superposition.'''
>>
>> Please could you explain further what it is I have misunderstood.
>>
>> Also would you say a progressive fit is a bad idea for more structured
>> proteins?
>>
>> Many thanks
>> James
>>
>> > Hi James,
>> >
>> > 'Spurious alignment' is the dependence of the resulting ensemble on
>> the
>> > reference structure. Unfortunately, that's not solved by a progressive
>> > fit.
>> > Rather, in a progressive fit, the same configuration can have multiple
>> > orientations, based on the previous structures, which is also
>> problematic
>> > when you're trying to understand spatial correlations between atoms
>> within
>> > their reference frame.
>> >
>> > Cheers,
>> >
>> > Tsjerk
>> >
>> > On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
>> >
>> >> Dear Teresa,
>> >>
>> >> That sounds like a periodic boundary issue to me. It could be fixed
>> by
>> >> using a tpr instead of a gro as the gmx covar manual says "All
>> >> structures
>> >> are fitted to the structure in the structure file. When this is not a
>> >> run
>> >> input file periodicity will not be taken into account." Alternatively
>> if
>> >> you don't have a tpr you could use gmx trjconv first with -pbc whole
>> or
>> >> -pbc nojump.
>> >>
>> >> I also remember reading (I think it was in the Hayward and de Groot
>> >> review
>> >> 2008) that fitting peptides to a reference structure can cause
>> spurious
>> >> alignments. I don't know if this is also related to what you're
>> seeing
>> >> but
>> >> it might be worth using gmx trjconv again with-fit progressive then
>> use
>> >> -nofit in gmx covar.
>> >>
>> >> Best wishes
>> >> James
>> >>
>> >> > Dear GROMACS community
>> >> >
>> >> > I am trying to complete a PCA analysis of my peptide adsorbed to a
>> >> > surface. However when I use :
>> >> >
>> >> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>> >> >
>> >> > and select the protein for both the least squares fit and
>> covariance
>> >> > calculation, followed by
>> >> >
>> >> >
>> >> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
>> >> > -first 1 -last 1 -skip 100
>> >> >
>> >> > and I select the peptide for the least squares and covariance
>> >> > calculation
>> >> >
>> >> > My peptide is now broken up into pieces. Is this right?
>> >> >
>> >> >
>> >> >
>> >> > Best
>> >> > Teresa
>> >> > --
>> >> > Gromacs Users mailing list
>> >> >
>> >> 

Re: [gmx-users] PCA problems

[Matthias Ernst]

In addition to what Tsjerk said, may I point out that a publication by a
colleague of mine treats exactly these problems that arise when trying
to fit cartesian structures:
http://scitation.aip.org/content/aip/journal/jcp/141/1/10.1063/1.4885338

Regards,
Matthias


On 06/08/2016 06:10 PM, Tsjerk Wassenaar wrote:
> Hi James,
> 
> That's silly! Ambiguous means that the same structure can have multiple
> solutions in a fit. The fit to a single reference structure (with more than
> three atoms) is never ambiguous. Can never, by definition!
> 
> Now if you have two reference structures at hand, and they have (quite)
> different structures, then fitting on one may give a different ensemble
> from fitting on the other. The fit is not consistent, and the inconsistency
> is worse for flexible molecules. Different ensembles will mean different
> correlations, thus giving different principal components.
> 
> Progressive fitting does not solve the problem. In fact, progressive
> fitting _is_ ambiguous. Let's say we have a series of conformations ABCAC.
> Then we  fit C once to B, which was fitted to A, and later we have C fitted
> to A, which was fitted to the previous C. Note that in practice the
> situation will be much worse as we can approach a certain configuration
> from many sides. Using B as reference will yield a fit that is different
> from using A as reference, so the structure C will have two different
> orientations in the resulting ensemble. Hence, the fit is ambiguous.
> 
> For structured proteins, the difference will not matter much. However, in
> long trajectories there may be an added contribution (drift) of the
> orientation.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On Wed, Jun 8, 2016 at 5:33 PM,  wrote:
> 
>> Thanks Tsjerk,
>>
>> Isn't the progressive fit supposed to rotate everything back into the same
>> orientation without having to worry about inferring that orientation from
>> a reference structure that doesn't align well? Each configuration should
>> in theory align well to its predecessor all the way back to the starting
>> structure (which is what I'd usually take as a reference anyway).
>>
>> The original note I was thinking of says as follows:
>>
>> '''Before a PCA, all structures should be superimposed onto a common
>> reference
>> structure. This can be problematic for very flexible systems such as
>> peptides,
>> where the fit may be ambiguous, leading to artificial structural
>> transitions. In
>> certain cases, such problems may be alleviated by using a progressive fit,
>> where
>> each structure is superimposed onto the previous one. It is also important
>> to note
>> that when results of different PCAs are to be compared with each other,
>> then
>> each individual PCA should be based on the same reference structure used
>> for
>> superposition.'''
>>
>> Please could you explain further what it is I have misunderstood.
>>
>> Also would you say a progressive fit is a bad idea for more structured
>> proteins?
>>
>> Many thanks
>> James
>>
>>> Hi James,
>>>
>>> 'Spurious alignment' is the dependence of the resulting ensemble on the
>>> reference structure. Unfortunately, that's not solved by a progressive
>>> fit.
>>> Rather, in a progressive fit, the same configuration can have multiple
>>> orientations, based on the previous structures, which is also problematic
>>> when you're trying to understand spatial correlations between atoms
>> within
>>> their reference frame.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
>>>
 Dear Teresa,

 That sounds like a periodic boundary issue to me. It could be fixed by
 using a tpr instead of a gro as the gmx covar manual says "All
 structures
 are fitted to the structure in the structure file. When this is not a
 run
 input file periodicity will not be taken into account." Alternatively if
 you don't have a tpr you could use gmx trjconv first with -pbc whole or
 -pbc nojump.

 I also remember reading (I think it was in the Hayward and de Groot
 review
 2008) that fitting peptides to a reference structure can cause spurious
 alignments. I don't know if this is also related to what you're seeing
 but
 it might be worth using gmx trjconv again with-fit progressive then use
 -nofit in gmx covar.

 Best wishes
 James

> Dear GROMACS community
>
> I am trying to complete a PCA analysis of my peptide adsorbed to a
> surface. However when I use :
>
> gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>
> and select the protein for both the least squares fit and covariance
> calculation, followed by
>
>
> gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> -first 1 -last 1 -skip 100
>
> and I select the peptide for the least squares and covariance
> calculation
>
> My peptide is now broken up into 

Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi James,

That's silly! Ambiguous means that the same structure can have multiple
solutions in a fit. The fit to a single reference structure (with more than
three atoms) is never ambiguous. Can never, by definition!

Now if you have two reference structures at hand, and they have (quite)
different structures, then fitting on one may give a different ensemble
from fitting on the other. The fit is not consistent, and the inconsistency
is worse for flexible molecules. Different ensembles will mean different
correlations, thus giving different principal components.

Progressive fitting does not solve the problem. In fact, progressive
fitting _is_ ambiguous. Let's say we have a series of conformations ABCAC.
Then we  fit C once to B, which was fitted to A, and later we have C fitted
to A, which was fitted to the previous C. Note that in practice the
situation will be much worse as we can approach a certain configuration
from many sides. Using B as reference will yield a fit that is different
from using A as reference, so the structure C will have two different
orientations in the resulting ensemble. Hence, the fit is ambiguous.

For structured proteins, the difference will not matter much. However, in
long trajectories there may be an added contribution (drift) of the
orientation.

Hope it helps,

Tsjerk

On Wed, Jun 8, 2016 at 5:33 PM,  wrote:

> Thanks Tsjerk,
>
> Isn't the progressive fit supposed to rotate everything back into the same
> orientation without having to worry about inferring that orientation from
> a reference structure that doesn't align well? Each configuration should
> in theory align well to its predecessor all the way back to the starting
> structure (which is what I'd usually take as a reference anyway).
>
> The original note I was thinking of says as follows:
>
> '''Before a PCA, all structures should be superimposed onto a common
> reference
> structure. This can be problematic for very flexible systems such as
> peptides,
> where the fit may be ambiguous, leading to artificial structural
> transitions. In
> certain cases, such problems may be alleviated by using a progressive fit,
> where
> each structure is superimposed onto the previous one. It is also important
> to note
> that when results of different PCAs are to be compared with each other,
> then
> each individual PCA should be based on the same reference structure used
> for
> superposition.'''
>
> Please could you explain further what it is I have misunderstood.
>
> Also would you say a progressive fit is a bad idea for more structured
> proteins?
>
> Many thanks
> James
>
> > Hi James,
> >
> > 'Spurious alignment' is the dependence of the resulting ensemble on the
> > reference structure. Unfortunately, that's not solved by a progressive
> > fit.
> > Rather, in a progressive fit, the same configuration can have multiple
> > orientations, based on the previous structures, which is also problematic
> > when you're trying to understand spatial correlations between atoms
> within
> > their reference frame.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
> >
> >> Dear Teresa,
> >>
> >> That sounds like a periodic boundary issue to me. It could be fixed by
> >> using a tpr instead of a gro as the gmx covar manual says "All
> >> structures
> >> are fitted to the structure in the structure file. When this is not a
> >> run
> >> input file periodicity will not be taken into account." Alternatively if
> >> you don't have a tpr you could use gmx trjconv first with -pbc whole or
> >> -pbc nojump.
> >>
> >> I also remember reading (I think it was in the Hayward and de Groot
> >> review
> >> 2008) that fitting peptides to a reference structure can cause spurious
> >> alignments. I don't know if this is also related to what you're seeing
> >> but
> >> it might be worth using gmx trjconv again with-fit progressive then use
> >> -nofit in gmx covar.
> >>
> >> Best wishes
> >> James
> >>
> >> > Dear GROMACS community
> >> >
> >> > I am trying to complete a PCA analysis of my peptide adsorbed to a
> >> > surface. However when I use :
> >> >
> >> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
> >> >
> >> > and select the protein for both the least squares fit and covariance
> >> > calculation, followed by
> >> >
> >> >
> >> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> >> > -first 1 -last 1 -skip 100
> >> >
> >> > and I select the peptide for the least squares and covariance
> >> > calculation
> >> >
> >> > My peptide is now broken up into pieces. Is this right?
> >> >
> >> >
> >> >
> >> > Best
> >> > Teresa
> >> > --
> >> > 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
> >> > 

Re: [gmx-users] PCA problems

[jkrieger]

Thanks Tsjerk,

Isn't the progressive fit supposed to rotate everything back into the same
orientation without having to worry about inferring that orientation from
a reference structure that doesn't align well? Each configuration should
in theory align well to its predecessor all the way back to the starting
structure (which is what I'd usually take as a reference anyway).

The original note I was thinking of says as follows:

'''Before a PCA, all structures should be superimposed onto a common
reference
structure. This can be problematic for very flexible systems such as
peptides,
where the fit may be ambiguous, leading to artificial structural
transitions. In
certain cases, such problems may be alleviated by using a progressive fit,
where
each structure is superimposed onto the previous one. It is also important
to note
that when results of different PCAs are to be compared with each other, then
each individual PCA should be based on the same reference structure used for
superposition.'''

Please could you explain further what it is I have misunderstood.

Also would you say a progressive fit is a bad idea for more structured
proteins?

Many thanks
James

> Hi James,
>
> 'Spurious alignment' is the dependence of the resulting ensemble on the
> reference structure. Unfortunately, that's not solved by a progressive
> fit.
> Rather, in a progressive fit, the same configuration can have multiple
> orientations, based on the previous structures, which is also problematic
> when you're trying to understand spatial correlations between atoms within
> their reference frame.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Jun 8, 2016 at 9:27 AM,  wrote:
>
>> Dear Teresa,
>>
>> That sounds like a periodic boundary issue to me. It could be fixed by
>> using a tpr instead of a gro as the gmx covar manual says "All
>> structures
>> are fitted to the structure in the structure file. When this is not a
>> run
>> input file periodicity will not be taken into account." Alternatively if
>> you don't have a tpr you could use gmx trjconv first with -pbc whole or
>> -pbc nojump.
>>
>> I also remember reading (I think it was in the Hayward and de Groot
>> review
>> 2008) that fitting peptides to a reference structure can cause spurious
>> alignments. I don't know if this is also related to what you're seeing
>> but
>> it might be worth using gmx trjconv again with-fit progressive then use
>> -nofit in gmx covar.
>>
>> Best wishes
>> James
>>
>> > Dear GROMACS community
>> >
>> > I am trying to complete a PCA analysis of my peptide adsorbed to a
>> > surface. However when I use :
>> >
>> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>> >
>> > and select the protein for both the least squares fit and covariance
>> > calculation, followed by
>> >
>> >
>> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
>> > -first 1 -last 1 -skip 100
>> >
>> > and I select the peptide for the least squares and covariance
>> > calculation
>> >
>> > My peptide is now broken up into pieces. Is this right?
>> >
>> >
>> >
>> > Best
>> > Teresa
>> > --
>> > 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.
>> >
>>
>> --
>> 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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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi James,

'Spurious alignment' is the dependence of the resulting ensemble on the
reference structure. Unfortunately, that's not solved by a progressive fit.
Rather, in a progressive fit, the same configuration can have multiple
orientations, based on the previous structures, which is also problematic
when you're trying to understand spatial correlations between atoms within
their reference frame.

Cheers,

Tsjerk

On Wed, Jun 8, 2016 at 9:27 AM,  wrote:

> Dear Teresa,
>
> That sounds like a periodic boundary issue to me. It could be fixed by
> using a tpr instead of a gro as the gmx covar manual says "All structures
> are fitted to the structure in the structure file. When this is not a run
> input file periodicity will not be taken into account." Alternatively if
> you don't have a tpr you could use gmx trjconv first with -pbc whole or
> -pbc nojump.
>
> I also remember reading (I think it was in the Hayward and de Groot review
> 2008) that fitting peptides to a reference structure can cause spurious
> alignments. I don't know if this is also related to what you're seeing but
> it might be worth using gmx trjconv again with-fit progressive then use
> -nofit in gmx covar.
>
> Best wishes
> James
>
> > Dear GROMACS community
> >
> > I am trying to complete a PCA analysis of my peptide adsorbed to a
> > surface. However when I use :
> >
> > gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
> >
> > and select the protein for both the least squares fit and covariance
> > calculation, followed by
> >
> >
> > gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> > -first 1 -last 1 -skip 100
> >
> > and I select the peptide for the least squares and covariance
> > calculation
> >
> > My peptide is now broken up into pieces. Is this right?
> >
> >
> >
> > Best
> > Teresa
> > --
> > 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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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send
> > a mail to gmx-users-requ...@gromacs.org.
> >
>
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Re: [gmx-users] PCA problems

[ingram]

Thanks very much for your help.

I have tried with a .tpr file and there is an improvement but still 
breaks. Similarly when I apply the same protocol as I said previously, 
but with my peptide unbound I get the same problem however in this case 
the free peptide has no pbc conditions


Best

Teresa

On 2016-06-08 09:27, jkrie...@mrc-lmb.cam.ac.uk wrote:

Dear Teresa,

That sounds like a periodic boundary issue to me. It could be fixed 
by
using a tpr instead of a gro as the gmx covar manual says "All 
structures
are fitted to the structure in the structure file. When this is not a 
run
input file periodicity will not be taken into account." Alternatively 
if
you don't have a tpr you could use gmx trjconv first with -pbc whole 
or

-pbc nojump.

I also remember reading (I think it was in the Hayward and de Groot 
review
2008) that fitting peptides to a reference structure can cause 
spurious
alignments. I don't know if this is also related to what you're 
seeing but
it might be worth using gmx trjconv again with-fit progressive then 
use

-nofit in gmx covar.

Best wishes
James


Dear GROMACS community

I am trying to complete a PCA analysis of my peptide adsorbed to a
surface. However when I use :

gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc

and select the protein for both the least squares fit and covariance
calculation, followed by


gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
-first 1 -last 1 -skip 100

and I select the peptide for the least squares and covariance
calculation

My peptide is now broken up into pieces. Is this right?



Best
Teresa
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Re: [gmx-users] PCA problems

[jkrieger]

Dear Teresa,

That sounds like a periodic boundary issue to me. It could be fixed by
using a tpr instead of a gro as the gmx covar manual says "All structures
are fitted to the structure in the structure file. When this is not a run
input file periodicity will not be taken into account." Alternatively if
you don't have a tpr you could use gmx trjconv first with -pbc whole or
-pbc nojump.

I also remember reading (I think it was in the Hayward and de Groot review
2008) that fitting peptides to a reference structure can cause spurious
alignments. I don't know if this is also related to what you're seeing but
it might be worth using gmx trjconv again with-fit progressive then use
-nofit in gmx covar.

Best wishes
James

> Dear GROMACS community
>
> I am trying to complete a PCA analysis of my peptide adsorbed to a
> surface. However when I use :
>
> gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>
> and select the protein for both the least squares fit and covariance
> calculation, followed by
>
>
> gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro
> -first 1 -last 1 -skip 100
>
> and I select the peptide for the least squares and covariance
> calculation
>
> My peptide is now broken up into pieces. Is this right?
>
>
>
> Best
> Teresa
> --
> 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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> a mail to gmx-users-requ...@gromacs.org.
>

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Re: [gmx-users] PCA problems

[Tsjerk Wassenaar]

Hi Teresa,

No, the peptide should not be broken. Did you remove jumps over PBC?
The peptide will probably be severely distorted by filtering, though.

Cheers,

Tsjerk


On Wed, Jun 8, 2016 at 8:49 AM, ingram  wrote:

> Dear GROMACS community
>
> I am trying to complete a PCA analysis of my peptide adsorbed to a
> surface. However when I use :
>
> gmx covar -s trajectory.gro  -f md_golp_vacuo.xtc
>
> and select the protein for both the least squares fit and covariance
> calculation, followed by
>
>
> gmx anaeig -s trajectory.gro -f md_golp_vacuo.trr -filt filter1.gro -first
> 1 -last 1 -skip 100
>
> and I select the peptide for the least squares and covariance calculation
>
> My peptide is now broken up into pieces. Is this right?
>
>
>
> Best
> Teresa
> --
> 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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>
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> 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.
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