[gmx-users] trjconv -fit rot+trans before a pbc? safe way to rotate a trajectory?

[Tsjerk Wassenaar]

Hi Camilo,

The things you desire are in principle possible, but they require code
reorganisation as well as quite a bit of additional coding that isn't
really worth the hassle. Probably it's actually better to split up
trjconv to have one tool for pbc related work and one for fitting
related options to make things more clear.

Cheers,

Tsjerk

On Mon, Jan 10, 2011 at 11:09 PM, Roland Schulz <roland at utk.edu> wrote:
>
>
> 2011/1/10 Camilo Andrés Jimenez Cruz <camilo.jimenezc at gmail.com>
>>
>> Hi list!
>> it has been discussed in other posts the inconvenience of PBCing after
>> rotating (see example:
>> http://oldwww.gromacs.org/pipermail/gmx-developers/2009-November/003754.html),
>> I just want to know what is the state of this problem and if somebody has
>> found a satisfying solution.
>> I also wonder if it has been considered the idea of doing PBC  *at the
>> same time* that the rotation is made, In my view, this would fix the
>> problem. no?
>
> No. At the same time doesn't make sense. You need one reference frame to do
> PBC. And it can't be rotated. In most cases (I give one example in the mail
> you linked where this is not the case) you can do first PBC and than fit.
> Roland
>>
>>
>>
>> Thanks!
>>
>> --
>> Camilo Andrés Jiménez Cruz
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands