[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.
>> -- 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-request at gromacs.org.
>>