[gmx-users] rotational fit in XY plane only

[Berk Hess]

Hi,

I would say that in most cases when you only want to remove rotation
in the xy plane, you also only want to remove translation in the xy plane.
But apparently for your system this is not the case.

I have just fixed a bug in the xy fit that could cause mirror imaging
of the system (I indeed had some D-amino peptides in my output).

Berk.

>From: "Itamar Kass" <ikass at uq.edu.au>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] rotational fit in XY plane only
>Date: Thu, 3 May 2007 15:13:18 +1000
>
>Hi,
>
>That what I did, I just hoped to be more lazy then I am already.
>
>Itamar
>
>----- Original Message ----- From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Sent: Thursday, May 03, 2007 2:31 PM
>Subject: Re: [gmx-users] rotational fit in XY plane only
>
>
>>Well, you can ofcourse run trjconv twice...
>>
>>Tsjerk
>>
>>On 5/3/07, Itamar Kass <ikass at uq.edu.au> wrote:
>>>Dear Berk,
>>>
>>>Thanks you very much for your quick and helpfully replay. If I may be a
>>>bit nudnik and ask to get it as "rotxy+transxyz" instated of
>>>"rotxy+transxy" thats will be wonderfully.
>>>
>>>Thanks, Itamar
>>>
>>>Best,
>>>Itamar
>>>
>>>Berk Hess wrote:
>>> >
>>> >
>>> >
>>> >> From: "Berk Hess" <gmx3 at hotmail.com>
>>> >> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >> To: gmx-users at gromacs.org
>>> >> Subject: RE: [gmx-users] rotational fit in XY plane only
>>> >> Date: Wed, 02 May 2007 14:10:59 +0200
>>> >>
>>> >>
>>> >>
>>> >>
>>> >>> From: Dr Itamar Kass <ikass at uq.edu.au>
>>> >>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >>> Subject: [gmx-users] rotational fit in XY plane only
>>> >>> Date: Wed, 02 May 2007 19:44:12 +0800
>>> >>>
>>> >>> Hi all,
>>> >>>
>>> >>> I study a protein which is moving toward an interface during my
>>> >>> simulation. In order to analyse the why the protein is bound to the
>>> >>> interface I want to fit all my results. There is no problem with
>>> >>> translational fit, but I want to do rotational fit only in the XY 
>>> >>> plane.
>>> >>> Is there a nice way of doing so?
>>> >>>
>>> >>> Best,
>>> >>> Itamar
>>> >>
>>> >>
>>> >> Currently there is not.
>>> >> I would like to have that feature as well.
>>> >
>>> >
>>> > I implemented an xy only fitting option for trjconv in the development
>>> > branch.
>>> >
>>> > Berk.
>>> >
>>> > _________________________________________________________________
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>>> >
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>>>--
>>>"Prediction is very difficult, especially about the future" - Niels Bohr
>>>
>>>===========================================
>>>| Itamar Kass, Ph.D.
>>>| Postdoctoral Research Fellow
>>>|
>>>| Molecular Dynamics Group
>>>| School of Molecular and Microbial Sciences (SMMS)
>>>| Chemistry Building (#68)
>>>| The University of Queensland
>>>| St. Lucia Campus, Brisbane, QLD 4067
>>>| Australia
>>>|
>>>| Tel: +61 7 3365 9922
>>>| Fax: +61 7 3365 3872
>>>| E-mail: ikass at uq.edu.au
>>>| Web page: http://www.uq.edu.au/~uqikass/
>>>| Personal web page: http://thekassfamily.blogspot.com/
>>>============================================
>>>
>>>Unless stated otherwise, this e-mail represents only the views of the
>>>Sender and not the views of The University of Queensland
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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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>>
>
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