[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, jkrieger at 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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