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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
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" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users" <[email protected]>
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 <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]>
>> Reply-To: Discussion list for GROMACS users <[email protected]>
>> To: [email protected]
>> Subject: RE: [gmx-users] rotational fit in XY plane only
>> Date: Wed, 02 May 2007 14:10:59 +0200
>>
>>
>>
>>
>>> From: Dr Itamar Kass <[EMAIL PROTECTED]>
>>> Reply-To: Discussion list for GROMACS users <[email protected]>
>>> To: Discussion list for GROMACS users <[email protected]>
>>> 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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--
"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
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|
| Tel: +61 7 3365 9922
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Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
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