[gmx-developers] Re: trjconv -fit rot+trans -pbc broken, was: trjconv defaults

[Tsjerk Wassenaar]

Hi Roland,

Doing PBC stuff first and fitting later is still the only solution.
Somewhere in the archive there is a discussion digging further on this
problem, but with exactly the same conclusion. There will still be a
difficulty with visualization though, if the box is to be rotated. The
PDB format does not allow inclusion of such arbitrary triclinic cells.
They can't be captured in a CRYST1 record, which has vector lengths
and angles, but not orientation.

Cheers,

Tsjerk

On Wed, Nov 4, 2009 at 8:35 PM, Roland Schulz <roland at utk.edu> wrote:
> Hi,
>
> sorry small correction to my last email:
>
> It is OK to do pbc first and then do trjconv -fit trans+rot. Different to
> what I wrote earlier it is correct that the rotation moves atoms out of the
> box because it is the wrong box (their are still in the correct box). To
> move them correctly in the translational shifted box you should do:
> trjconv -fit translation -pbc {some-pbc}
> trjconv -fit rot+trans
>
> This guarantees that the pbc treatment is correct in the original box.
>
> But the problem persists if you need pbc treatment in the
> tools/visualization you use after trjconv. Since the written box vectors are
> not rotated any pbc treatment applied to that trajectory will be wrong.
>
> So I still think the only real solution is the one proposed by Tsjerk. I
> just wanted to add that there is a partial work-around.
>
> Roland
>
> On Wed, Nov 4, 2009 at 2:00 PM, Roland Schulz <roland at utk.edu> wrote:
>>
>> Hi,
>>
>> I'm replaying here to a year old thread because I found Tsjerk desribing a
>> problem I'm currently having and I think no fix is so far planned.
>>
>> As he describes below if you do a fit then a later pbc correction is wrong
>> because the box vectors don't get rotated together with the system.
>>
>> But this problem is not only introduced by changed defaults (as -ur
>> compact) but is a problem with any -ur.
>>
>> Whenever one does a trjconv -fit rot+trans -pbc [any pbc] the pbc
>> correction is wrong because the box vectors are wrong.
>>
>> Doing the pbc before is not a work-around because the rotation might move
>> molecules out of the box again. Also first doing the fit and the calling
>> trjconv again for -pbc does not work because the saved box vectors are the
>> wrong (unrotated) ones and thus the pbc still are wrong.
>>
>> The only fix I see is Tsjerk's solution to also rotate the box vectors. Or
>> is there any other solution?
>>
>> Roland
>>
>>
>> On Fri, Oct 17, 2008 at 4:02 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
>> wrote:
>>>
>>> Hi,
>>>
>>> No!
>>>
>>> I was already typing that I was in favour of setting -pbc to whole by
>>> default, but not -ur compact, when the following struck me: Setting
>>> these to defaults will screw up any trajectory/pdb which has before
>>> been processed with options causing discrepancy between configuration
>>> and pbc. In normal words, whenever you've performed a fit, you'll only
>>> end up with garbled output running trjconv again.
>>>
>>> The solution to that, and I mentioned that to Erik at the workshop,
>>> would be to have all fitting and other reorienting procedures also
>>> perform on the box. That's a minor change, but then again, we have to
>>> get rid of the 'box too skewed' error in analysis tools and be
>>> prepared to use all nine numbers in the box matrix for the definition
>>> of the PBC. Note that this doesn't work for PDB files, and there is no
>>> work-around.
>>>
>>> In the margin of that, I also disfavour having the default for -ur set
>>> to compact, because it will give unnecessary computational overhead
>>> when processing trajectory files for whatever. Resetting to a
>>> rectangular brick (or triclinic cell) on the other hand, is trivial.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Fri, Oct 17, 2008 at 10:19 AM, David van der Spoel
>>> <spoel at xray.bmc.uu.se> wrote:
>>> > Hi,
>>> >
>>> > shall we set the trjconv defaults to -pbc mol -ur compact ?
>>> > Even I get fooled when dumping a pdb file and suddenly noticing that it
>>> > is
>>> > broken.
>>> >
>>> > Cheers,
>>> > --
>>> > David.
>>> >
>>> > ________________________________________________________________________
>>> > David van der Spoel, PhD, Professor of Biology
>>> > Dept. of Cell and Molecular Biology, Uppsala University.
>>> > Husargatan 3, Box 596,          75124 Uppsala, Sweden
>>> > phone:  46 18 471 4205          fax: 46 18 511 755
>>> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
>>> >
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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
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>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
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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