Hi,<br><br>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.<br><br>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.<br>
<br>But this problem is not only introduced by changed defaults (as -ur compact) but is a problem with any -ur.<br><br>Whenever one does a trjconv -fit rot+trans -pbc [any pbc] the pbc correction is wrong because the box vectors are wrong.<br>
<br>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.<br>
<br>The only fix I see is Tsjerk's solution to also rotate the box vectors. Or is there any other solution?<br><br>Roland<br><br><br><div class="gmail_quote">On Fri, Oct 17, 2008 at 4:02 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>
<br>
No!<br>
<br>
I was already typing that I was in favour of setting -pbc to whole by<br>
default, but not -ur compact, when the following struck me: Setting<br>
these to defaults will screw up any trajectory/pdb which has before<br>
been processed with options causing discrepancy between configuration<br>
and pbc. In normal words, whenever you've performed a fit, you'll only<br>
end up with garbled output running trjconv again.<br>
<br>
The solution to that, and I mentioned that to Erik at the workshop,<br>
would be to have all fitting and other reorienting procedures also<br>
perform on the box. That's a minor change, but then again, we have to<br>
get rid of the 'box too skewed' error in analysis tools and be<br>
prepared to use all nine numbers in the box matrix for the definition<br>
of the PBC. Note that this doesn't work for PDB files, and there is no<br>
work-around.<br>
<br>
In the margin of that, I also disfavour having the default for -ur set<br>
to compact, because it will give unnecessary computational overhead<br>
when processing trajectory files for whatever. Resetting to a<br>
rectangular brick (or triclinic cell) on the other hand, is trivial.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Fri, Oct 17, 2008 at 10:19 AM, David van der Spoel<br>
<<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>
> Hi,<br>
><br>
> shall we set the trjconv defaults to -pbc mol -ur compact ?<br>
> Even I get fooled when dumping a pdb file and suddenly noticing that it is<br>
> broken.<br>
><br>
> Cheers,<br>
> --<br>
> David.<br>
> ________________________________________________________________________<br>
> David van der Spoel, PhD, Professor of Biology<br>
> Dept. of Cell and Molecular Biology, Uppsala University.<br>
> Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>
> phone: 46 18 471 4205 fax: 46 18 511 755<br>
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<br>
<br>
</div></div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
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