[gmx-users] problem fitting trajectory

[Tsjerk Wassenaar]

Hi,

It is better to do PBC options first and fitting options after, with
separate calls to trjconv. Fitting and PBC don't go well together,
This has been elaborately discussed on the mailing list before.

Cheers,

Tsjerk

On Wed, Jun 10, 2009 at 8:59 PM, Justin A. Lemkul<jalemkul at vt.edu> wrote:
>
> I have found that the combination of -pbc mol -ur compact always looks
> pretty :)  So in addition to -fit and perhaps -center, try those two options
> together.
>
> -Justin
>
> Rebeca García Fandiño wrote:
>>
>> Hello,
>> I have done a simulation using Gromacs 4 (4.0.2) and I would like to have
>> a trajectory were the protein is fitted to the first structure (to mantain
>> the exact orientation).
>>
>> When I have tried
>>
>> echo 1 1 0 | trjconv -f production_1_3.xtc -s production1.tpr -center -fit
>> rot+trans -pbc mol -o production_1_3_fit.xtc
>>
>> visualizing production_1_3_fit.xtc I can see that the protein is fitted,
>> however there are a lot of "holes" into the water box. It seems like the pbc
>> were not correctly applied. I have tried changing a lot of options (-pbc
>> res, -boxcenter rect,...) but nothing works.
>>
>> The options
>>
>> trjconv -f production_1_3.xtc -s production1.tpr -center -boxcenter rect
>> -fit rot+trans -pbc mol -o production_1_3_fit.xtc
>>
>> do not produce any hole in the box of water, but the box entirely moves
>> around the protein, and sometimes it is outside of it and not solvated.
>>
>> I have also tried using Gromacs 4.0.4, but the problem is still the same.
>>
>> Could anybody give an idea of how solving it, please?
>>
>> Thank you very much for your help.
>>
>> Best wishes,
>>
>> Rebeca Garcia
>> Academic Visitor
>> Oxford University
>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623